CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 173

2023-06-25T23:47:25Z

Mario Murakami:

{{CuratorApproved}}
* [[Author]]s: [[User:Clelton Santos|Clelton Aparecido dos Santos]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH173'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining (inferred)
|-
|'''Active site residues'''
|known (inferred)
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH173.html
|}
</div>


== Substrate specificities ==
The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families [[GH2]] and [[GH78]], remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a [[GH36]] domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families [[GH30]] and [[GH5]] <cite>Cabral2022</cite>.

== Kinetics and Mechanism ==
GH173 members are inferred to be retaining enzymes <cite>Cabral2022</cite>.

== Catalytic Residues ==
The residues E305 and E207 (sequence numbering based on the founding member, CapGH173) was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models <cite>Cabral2022</cite>.

== Three-dimensional structures ==
Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the [[GH30]] family. Except for the residues defining the clan GH-A, sequence alignment with [[GH5]] and [[GH30]] members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.  

== Family Firsts ==
;First stereochemistry determination: CapGH173 is inferred to operate by a retaining mechanism.
;First catalytic nucleophile identification: E305 (inferred).
;First general acid/base residue identification: E207 (inferred).
;First 3-D structure: Currently no experimental structure is available for GH173 members.

== References ==
<biblio>

#Cabral2022 pmid=35110564
</biblio>

[[Category:Glycoside Hydrolase Families|GH173]]

Carbohydrate Binding Module Family 89

2023-06-25T23:46:40Z

Mario Murakami:

{{CuratorApproved}}
* [[Author]]s: [[User:Mariana Morais|Mariana Abrahão Bueno de Morais]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM89.html
|}
</div>


== Ligand specificities ==
The CBM89 family was created based on the discovery of an N-terminal domain appended to a GH10 xylanase recovered from a metagenome-assembled genome (MAG) of the capybara gut microbiota. The founding member, CapCBM89, was shown to interact with beechwood xylan and rye arabinoxylan according to affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural architectures have been found in the families GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 on the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>..

* '''Features of ligand binding:''' A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The founding member, [https://www.ncbi.nlm.nih.gov/protein/UMW87592.1 CapCBM89], was found appended to the N-terminus of a GH10 domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-GH10 and two exo-acting enzymes from [https://www.ncbi.nlm.nih.gov/protein/2205462650 GH43] and [https://www.ncbi.nlm.nih.gov/protein/2205462646 GH97] families <cite>Cabral2022</cite>. The GH10 domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the GH10 domain to these substrates catalysis <cite>Cabral2022</cite>.

* '''Most Common Associated Modules:''' 1. Glycoside hydrolases from the GH10 family.

== Family Firsts ==

*'''First Identified:''' The first identified CBM89 member (CapCBM89) was from an uncultured Bacteroidaceae MAG57 recovered from the capybara gut microbiome <cite>Cabral2022</cite> .

*'''First Structural Characterization:''' The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .

== References ==
<biblio>
#Cabral2022 pmid=35110564

</biblio>


[[Category:Carbohydrate Binding Module Families|CBM089]]

Carbohydrate Binding Module Family 89

2023-06-22T12:40:05Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]s: [[User:Mariana Morais|Mariana Abrahão Bueno de Morais]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM89.html
|}
</div>


== Ligand specificities ==
The CBM89 family was created based on the discovery of an N-terminal domain appended to a GH10 xylanase recovered from a metagenome-assembled genome (MAG) of the capybara gut microbiota. The founding member, CapCBM89, was shown to interact with beechwood xylan and rye arabinoxylan according to affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural architectures have been found in the families GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 on the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>..

* '''Features of ligand binding:''' A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The founding member, CapCBM89, was found appended to the N-terminus of a GH10 domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-GH10 and two exo-acting enzymes from GH43 and GH97 families <cite>Cabral2022</cite>. The GH10 domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the GH10 domain to these substrates catalysis <cite>Cabral2022</cite>.

* '''Most Common Associated Modules:''' 1. Glycoside hydrolases from the GH10 family.

== Family Firsts ==

*'''First Identified:''' The first identified CBM89 member (CapCBM89) was from a Bacteroidaceae MAG retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .

*'''First Structural Characterization:''' The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .

== References ==
<biblio>
#Cabral2022 pmid=35110564

</biblio>


[[Category:Carbohydrate Binding Module Families|CBM089]]

Carbohydrate Binding Module Family 89

2023-06-22T12:24:00Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]s: [[User:Mariana Morais|Mariana Abrahão Bueno de Morais]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM89.html
|}
</div>


== Ligand specificities ==
The CBM89 family was created based on the discovery of an N-terminal domain appended to a GH10 xylanase recovered from a metagenome-assembled genome (MAG) of the capybara gut microbiota. The founding member, CapCBM89, was shown to interact with beechwood xylan and rye arabinoxylan according to affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural architectures have been found in the families GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 on the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>..

* '''Features of ligand binding:''' A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The founding member, CapCBM89, was found appended to the N-terminus of a GH10 domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-GH10 and two exo-acting enzymes from GH43 and GH97 families <cite>Cabral2022</cite>. The GH10 domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the GH10 domain to these substrates catalysis <cite>Cabral2022</cite>.

* '''Most Common Associated Modules:''' 1. Glycoside hydrolases from the GH10 family.

== Family Firsts ==

*'''First Identified:''' The first CBM89 member to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <cite>Cabral2022</cite> .

*'''First Structural Characterization:''' The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .

== References ==
<biblio>
#Cabral2022 pmid=35110564

</biblio>


[[Category:Carbohydrate Binding Module Families|CBM089]]

Glycoside Hydrolase Family 173

2023-06-21T12:59:11Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]s: [[User:Clelton Santos|Clelton Aparecido dos Santos]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH173'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining (inferred)
|-
|'''Active site residues'''
|known (inferred)
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH173.html
|}
</div>


== Substrate specificities ==
The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.

== Kinetics and Mechanism ==
GH173 members are inferred to be retaining enzymes <cite>Cabral2022</cite>.

== Catalytic Residues ==
The residues E305 and E207 (sequence numbering based on the founding member, CapGH173) was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models <cite>Cabral2022</cite>.

== Three-dimensional structures ==
Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.  

== Family Firsts ==
;First stereochemistry determination: CapGH173 is inferred to operate by a retaining mechanism.
;First catalytic nucleophile identification: E305 (inferred).
;First general acid/base residue identification: E207 (inferred).
;First 3-D structure: Currently no experimental structure is available for GH173 members.

== References ==
<biblio>

#Cabral2022 pmid=35110564
</biblio>

[[Category:Glycoside Hydrolase Families|GH173]]

Glycoside Hydrolase Family 173

2023-06-21T12:41:00Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]s: [[User:Clelton Santos|Clelton Aparecido dos Santos]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH173'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining (inferred)
|-
|'''Active site residues'''
|known (inferred)
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH173.html
|}
</div>


== Substrate specificities ==
The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.

== Kinetics and Mechanism ==
GH173 members are inferred to be retaining enzymes <cite>Cabral2022</cite>.

== Catalytic Residues ==
The residues E305 and E207 was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models <cite>Cabral2022</cite>.

== Three-dimensional structures ==
Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.  

== Family Firsts ==
;First stereochemistry determination: CapGH173 is inferred to operate by a retaining mechanism.
;First catalytic nucleophile identification: E305 (inferred).
;First general acid/base residue identification: E207 (inferred).
;First 3-D structure: Currently no experimental structure is available for GH173 members.

== References ==
<biblio>

#Cabral2022 pmid=35110564
</biblio>

[[Category:Glycoside Hydrolase Families|GH173]]

Glycoside Hydrolase Family 173

2023-06-21T12:40:34Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]s: [[User:Clelton Santos|Clelton Aparecido dos Santos]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH173'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining (inferred)
|-
|'''Active site residues'''
|known (inferred)
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH173.html
|}
</div>


== Substrate specificities ==
The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.

== Kinetics and Mechanism ==
GH173 members are inferred to be retaining enzymes <cite>Cabral2022</cite>.

== Catalytic Residues ==
The residues E305 and E207 was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models (<cite>Cabral2022</cite>).

== Three-dimensional structures ==
Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.  

== Family Firsts ==
;First stereochemistry determination: CapGH173 is inferred to operate by a retaining mechanism.
;First catalytic nucleophile identification: E305 (inferred).
;First general acid/base residue identification: E207 (inferred).
;First 3-D structure: Currently no experimental structure is available for GH173 members.

== References ==
<biblio>

#Cabral2022 pmid=35110564
</biblio>

[[Category:Glycoside Hydrolase Families|GH173]]

Glycoside Hydrolase Family 128

2020-09-29T11:38:47Z

Mario Murakami:

* [[Author]]: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
* [[Responsible Curator]]: ^^^Mario Murakami^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH128'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH128.html
|}
</div>


== Substrate specificity and modes of action ==
The first GH128 enzyme, GLU1, was cloned from ''Lentinula edodes'' fruiting bodies (shiitake mushroom) <cite>Sakamoto2011</cite>. GLU1 cleaves β-1,3 linkages in various β-glucans such as endogenous ''L. edodes'' lentinan, laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis'', but does not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. Further work with several GH128 members corroborated that this family is specific for β-1,3-glucans <cite>Santos2020</cite>. Bacterial members from ''Amycolatopsis mediterranei'' (subgroup I) and ''Pseudomonas viridiflava'' (subgroup II)exhibit endo-β-1,3-glucanase activity and catalytic rates notably higher than those observed for fungal members <cite>Santos2020</cite>. On the other hand, fungal members display diverse modes of action and substrate specificity. The GH128 members from ''Aureobsidium namibiae'' (subgroup VI) and ''Cryptococcus neoformans'' (subgroup V) are exo-β-1,3-glucanases and release trisaccharides and monosaccharides from the reducing ends, respectively. The enzyme from ''Blastomyces gilchristii'' (subgroup III) is also an exo-β-1,3-glucanase; however, it releases trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans. The founder member of the family, GLU1 from ''L. edodes'' (subgroup IV) is an endo-β-1,3-glucanase with an atypical mode of substrate recognition as in the subgroup VI. Intriguingly, some fungal members from this family, such as those from ''Trichoderma gamsii'' and ''C. neoformans'', are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) <cite>Santos2020</cite>.

=== Clustering of GH128 ===
[[Image:Santos_GH128_final.png|thumb|right|250px|Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from <cite>Santos2020</cite>.]]
GH128 was created based on the study of ^^^Yuichi Sakamoto^^^ and colleagues <cite>Sakamoto2011</cite>. Years later, a group headed by ^^^Mario Murakami^^^ explored the functional and structural diversity of this family <cite>Santos2020</cite>. For this purpose, they employed phylogenetic and Sequence Similarity Network (SSN, <cite>Atkinson2009</cite>) analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two discrete clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). At least one member of each subgroup was biochemically and structurally characterized. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, feature a substrate-interacting "hydrophobic knuckle" (see [[#Three-dimensional structures]]) and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological functions (nutrition and competition). Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of strategies for substrate recognition (flattening mechanism – subgroups IV and VI; and hydrophobic knuckle – subgroups III, V and VII) and modes of action (exo-enzymes – subgroups III, V and VI; endo-enzymes – subgroup IV; and oligosaccharide binding proteins – subgroup VII).

== Kinetics and Mechanism ==
As indicated by the first study of a GH128 enzyme <cite>Sakamoto2011</cite>, this family is part of [[Clan]] GH-A, thus suggesting that its members operate by a classical Koshland [[retaining]] mechanism. This prediction was confirmed through <sup>1</sup>H-nuclear magnetic resonance spectroscopy of enzymatic products <cite>Santos2020</cite>.

== Catalytic Residues ==
From the sequence alignment of GH128 members, two glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the catalytic residues <cite>Sakamoto2011</cite>. They were further confirmed to be the [[general acid/base]] and the [[catalytic nucleophile]], respectively, by site-directed mutagenesis of the bacterial GH128 member from ''A. mediterranei'' <cite>Santos2020</cite>. These residues are located at the C-terminal ends of the strands β7 and β4 <cite>Santos2020</cite>, as observed for other [[clan]] GH-A families.

== Three-dimensional structures ==
A three-dimensional homology model of ''L. edodes'' GLU1 indicated similarity with several (β/α)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] β-xylosidase and a [[GH5]] β-mannanase <cite>Sakamoto2011</cite>. The fold resembling an (β/α)<sub>8</sub>-barrel was further confirmed with the crystal structure determination of 9 members of the family <cite>Santos2020</cite>. However, in all structures, the helix α2 and the strand β3 are strictly absent <cite>Santos2020</cite>. Moreover, some enzymes such as the endo-β-1,3-glucanase from ''L. edodes'' (GLU1) and the exo-β-1,3-glucanase from ''C. neoformans'', also lack the helices α1 and α3, respectively <cite>Santos2020</cite>.

Two distinct modes of substrate binding were observed in the GH128 family <cite>Santos2020</cite>. The most widespread mode, termed as "hydrophobic knuckle", involves a tryptophan residue that interacts with four glucoside moieties from –5 to –2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties –2 and –3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is referred to as the "flattening" mechanism, due to the unusual, but also stereochemically favorable, conformation adopted by the substrate. It is notable that this mode of substrate binding has not been observed in other CAZy families active on β-1,3-glucans.

== Family Firsts ==
;First stereochemistry determination: predicted to be retaining by membership in Clan GH-A <cite>Sakamoto2011</cite> and further validated by <sup>1</sup>H-NMR analysis of laminarin products generated by the ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First catalytic nucleophile identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First general acid/base residue identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First 3-D structure: predicted by modelling of ''L. edodes'' GLU1 <cite>Sakamoto2011</cite> and experimentally determined for several GH128 members including endo-β-1,3-glucanases from ''A. mediterranei'' (AmGH128_I), ''P. viridiflava'' (PvGH128_II), ''Sorangium cellulosum'' (ScGH128_II) and ''L. edodes'' (LeGH128_IV); exo-β-1,3-glucanases from ''B. gilchristii'' (BgGH128_III), ''C. neoformans'' (CnGH128_V) and ''A. namibiae'' (AnGH128_VI); and β-1,3-glucooligosaccharide binding proteins from ''T. gamsii'' (TgGH128_VII) and ''C. neoformans'' (CnGH128_VII) <cite>Santos2020</cite>.

== References ==
<biblio>

#Sakamoto2011 pmid=21965406
#Santos2020 pmid=32451508
#Atkinson2009 pmid=19190775

</biblio>

[[Category:Glycoside Hydrolase Families|GH128]]

Glycoside Hydrolase Family 128

2020-09-29T11:30:45Z

Mario Murakami:

* [[Author]]: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
* [[Responsible Curator]]: ^^^Mario Murakami^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH128'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH128.html
|}
</div>


== Substrate specificity and modes of action ==
The first GH128 enzyme, GLU1, was cloned from ''Lentinula edodes'' fruiting bodies (shiitake mushroom) <cite>Sakamoto2011</cite>. GLU1 cleaves β-1,3 linkages in various β-glucans such as endogenous ''L. edodes'' lentinan, laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis'', but does not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. Further work with several GH128 members corroborated that this family is specific for β-1,3-glucans <cite>Santos2020</cite>. Bacterial members from ''Amycolatopsis mediterranei'' (subgroup I) and ''Pseudomonas viridiflava'' (subgroup II)exhibit endo-β-1,3-glucanase activity and catalytic rates notably higher than those observed for fungal members <cite>Santos2020</cite>. On the other hand, fungal members display diverse modes of action and substrate specificity. The GH128 members from ''Aureobsidium namibiae'' (subgroup VI) and ''Cryptococcus neoformans'' (subgroup V) are exo-β-1,3-glucanases and release trisaccharides and monosaccharides from the reducing ends, respectively. The enzyme from ''Blastomyces gilchristii'' (subgroup III) is also an exo-β-1,3-glucanase; however, it releases trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans. The founder member of the family, GLU1 from ''L. edodes'' (subgroup IV) is an endo-β-1,3-glucanase with an atypical mode of substrate recognition as in the subgroup VI. Intriguingly, some fungal members from this family, such as those from ''Trichoderma gamsii'' and ''C. neoformans'', are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) <cite>Santos2020</cite>.

=== Clustering of GH128 ===
[[Image:Santos_GH128_final.png|thumb|right|250px|Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from <cite>Santos2020</cite>.]]
GH128 was created based on the study of ^^^Yuichi Sakamoto^^^ and colleagues <cite>Sakamoto2011</cite>. Years later, a group headed by ^^^Mario Murakami^^^ explored the functional and structural diversity of this family <cite>Santos2020</cite>. For this purpose, they employed phylogenetic and Sequence Similarity Network (SSN, <cite>Atkinson2009</cite>) analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two discrete clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). At least one member of each subgroup was biochemically and structurally characterized. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, feature a substrate-interacting "hydrophobic knuckle" (see [[#Three-dimensional structures]]) and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological functions (nutrition and competition). Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of strategies for substrate recognition (flattening mechanism – subgroups IV and VI; and hydrophobic knuckle – subgroups III, V and VII) and modes of action (exo-enzymes – subgroups III, V and VI; endo-enzymes – subgroup IV; and oligosaccharide binding proteins – subgroup VII).

== Kinetics and Mechanism ==
As indicated by the first study of a GH128 enzyme <cite>Sakamoto2011</cite>, this family is part of [[Clan]] GH-A, thus suggesting that its members operate by a classical Koshland [[retaining]] mechanism. This prediction was confirmed through <sup>1</sup>H-nuclear magnetic resonance spectroscopy of enzymatic products <cite>Santos2020</cite>.

== Catalytic Residues ==
From the sequence alignment of GH128 members, two glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the catalytic residues <cite>Sakamoto2011</cite>. They were further confirmed to be the [[general acid/base]] and the [[catalytic nucleophile]], respectively, by site-directed mutagenesis of the bacterial GH128 member from ''A. mediterranei'' <cite>Santos2020</cite>. These residues are located at the C-terminal ends of the strands β7 and β4 <cite>Santos2020</cite>, as observed for other [[clan]] GH-A families.

== Three-dimensional structures ==
A three-dimensional homology model of ''L. edodes'' GLU1 indicated similarity with several (β/α)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] β-xylosidase and a [[GH5]] β-mannanase <cite>Sakamoto2011</cite>. The fold resembling an (β/α)<sub>8</sub>-barrel was further confirmed with the crystal structure determination of 9 members of the family <cite>Santos2020</cite>. However, in all structures, the helix α2 and the strand β3 are strictly absent <cite>Santos2020</cite>. Moreover, some enzymes such as the endo-β-1,3-glucanase from ''L. edodes'' (GLU1) and the exo-β-1,3-glucanase from ''C. neoformans'', also lack the helices α1 and α3, respectively <cite>Santos2020</cite>.

Two distinct modes of substrate binding were observed in the GH128 family <cite>Santos2020</cite>. The most widespread mode, termed as "hydrophobic knuckle", involves a tryptophan residue that interacts with four glucoside moieties from –5 to –2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties –2 and –3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is referred to as the "flattening" mechanism, due to the unusual, but also stereochemically favorable, conformation adopted by the substrate. It is notable that this mode of substrate binding has not been observed in other CAZy families active on β-1,3-glucans.

== Family Firsts ==
;First stereochemistry determination: predicted to be retaining by membership in Clan GH-A <cite>Sakamoto2011</cite> and further validated by <sup>1</sup>H-NMR of products of the ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First catalytic nucleophile identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First general acid/base residue identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First 3-D structure: predicted by modelling of ''L. edodes'' GLU1 <cite>Sakamoto2011</cite> and experimentally determined for several GH128 members including endo-β-1,3-glucanases from ''A. mediterranei'' (AmGH128_I), ''P. viridiflava'' (PvGH128_II), ''Sorangium cellulosum'' (ScGH128_II) and ''L. edodes'' (LeGH128_IV); exo-β-1,3-glucanases from ''B. gilchristii'' (BgGH128_III), ''C. neoformans'' (CnGH128_V) and ''A. namibiae'' (AnGH128_VI); and β-1,3-glucooligosaccharide binding proteins from ''T. gamsii'' (TgGH128_VII) and ''C. neoformans'' (CnGH128_VII) <cite>Santos2020</cite>.

== References ==
<biblio>

#Sakamoto2011 pmid=21965406
#Santos2020 pmid=32451508
#Atkinson2009 pmid=19190775

</biblio>

[[Category:Glycoside Hydrolase Families|GH128]]

Glycoside Hydrolase Family 128

2020-09-29T11:26:38Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
* [[Responsible Curator]]: ^^^Mario Murakami^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH128'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH128.html
|}
</div>


== Substrate specificity and modes of action ==
The first GH128 enzyme, GLU1, was cloned from ''Lentinula edodes'' fruiting bodies (shiitake mushroom) <cite>Sakamoto2011</cite>. GLU1 cleaves β-1,3 linkages in various β-glucans such as endogenous ''L. edodes'' lentinan, laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis'', but does not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. Further work with several GH128 members corroborated that this family is specific for β-1,3-glucans <cite>Santos2020</cite>. Bacterial members from ''Amycolatopsis mediterranei'' (subgroup I) and ''Pseudomonas viridiflava'' (subgroup II)exhibit endo-β-1,3-glucanase activity and catalytic rates notably higher than those observed for fungal members <cite>Santos2020</cite>. On the other hand, fungal members display diverse modes of action and substrate specificity. The GH128 members from ''Aureobsidium namibiae'' (subgroup VI) and ''Cryptococcus neoformans'' (subgroup V) are exo-β-1,3-glucanases and release trisaccharides and monosaccharides from the reducing ends, respectively. The enzyme from ''Blastomyces gilchristii'' (subgroup III) is also an exo-β-1,3-glucanase; however, it releases trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans. The founder member of the family, GLU1 from ''L. edodes'' (subgroup IV) is an endo-β-1,3-glucanase with an atypical mode of substrate recognition as in the subgroup VI. Intriguingly, some fungal members from this family, such as those from ''Trichoderma gamsii'' and ''C. neoformans'', are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) <cite>Santos2020</cite>.

=== Clustering of GH128 ===
[[Image:Santos_GH128_final.png|thumb|right|250px|Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from <cite>Santos2020</cite>.]]
GH128 was created based on the study of ^^^Yuichi Sakamoto^^^ and colleagues <cite>Sakamoto2011</cite>. Years later, a group headed by ^^^Mario Murakami^^^ explored the functional and structural diversity of this family <cite>Santos2020</cite>. For this purpose, they employed phylogenetic and Sequence Similarity Network (SSN, <cite>Atkinson2009</cite>) analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two discrete clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). At least one member of each subgroup was biochemically and structurally characterized. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, feature a substrate-interacting "hydrophobic knuckle" (see [[#Three-dimensional structures]]) and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological functions (nutrition and competition). Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of strategies for substrate recognition (flattening mechanism – subgroups IV and VI; and hydrophobic knuckle – subgroups III, V and VII) and modes of action (exo-enzymes – subgroups III, V and VI; endo-enzymes – subgroup IV; and oligosaccharide binding proteins – subgroup VII).

== Kinetics and Mechanism ==
As indicated by the first study of a GH128 enzyme <cite>Sakamoto2011</cite>, this family is part of [[Clan]] GH-A, thus suggesting that its members operate by a classical Koshland [[retaining]] mechanism. This prediction was confirmed through <sup>1</sup>H-nuclear magnetic resonance spectroscopy of enzymatic products <cite>Santos2020</cite>.

== Catalytic Residues ==
From the sequence alignment of GH128 members, two glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the catalytic residues <cite>Sakamoto2011</cite>. They were further confirmed to be the [[general acid/base]] and the [[catalytic nucleophile]], respectively, by site-directed mutagenesis of the bacterial GH128 member from ''A. mediterranei'' <cite>Santos2020</cite>. These residues are located at the C-terminal ends of the strands β7 and β4 <cite>Santos2020</cite>, as observed for other [[clan]] GH-A families.

== Three-dimensional structures ==
A three-dimensional homology model of ''L. edodes'' GLU1 indicated similarity with several (β/α)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] β-xylosidase and a [[GH5]] β-mannanase <cite>Sakamoto2011</cite>. The fold resembling an (β/α)<sub>8</sub>-barrel was further confirmed with the crystal structure determination of 9 members of the family <cite>Santos2020</cite>. However, in all structures, the helix α2 and the strand β3 are strictly absent <cite>Santos2020</cite>. Moreover, some enzymes such as the endo-β-1,3-glucanase from ''L. edodes'' (GLU1) and the exo-β-1,3-glucanase from ''C. neoformans'', also lack the helices α1 and α3, respectively <cite>Santos2020</cite>.

Two distinct modes of substrate binding were observed in the GH128 family <cite>Santos2020</cite>. The most widespread mode, termed the "hydrophobic knuckle", involves a tryptophan residue that interacts with four glucoside moieties from –5 to –2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties –2 and –3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is referred to as the "flattening" mechanism, due to the unusual, but also stereochemically favorable, conformation adopted by the substrate. It is notable that this mode of substrate binding has not been observed in other CAZy families active on β-1,3-glucans.

== Family Firsts ==
;First stereochemistry determination: predicted to be retaining by membership in Clan GH-A <cite>Sakamoto2011</cite> and further validated by <sup>1</sup>H-NMR of products of the ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First catalytic nucleophile identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First general acid/base residue identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First 3-D structure: predicted by modelling of ''L. edodes'' GLU1 <cite>Sakamoto2011</cite> and experimentally determined for several GH128 members including endo-β-1,3-glucanases from ''A. mediterranei'' (AmGH128_I), ''P. viridiflava'' (PvGH128_II), ''Sorangium cellulosum'' (ScGH128_II) and ''L. edodes'' (LeGH128_IV); exo-β-1,3-glucanases from ''B. gilchristii'' (BgGH128_III), ''C. neoformans'' (CnGH128_V) and ''A. namibiae'' (AnGH128_VI); and β-1,3-glucooligosaccharide binding proteins from ''T. gamsii'' (TgGH128_VII) and ''C. neoformans'' (CnGH128_VII) <cite>Santos2020</cite>.

== References ==
<biblio>

#Sakamoto2011 pmid=21965406
#Santos2020 pmid=32451508
#Atkinson2009 pmid=19190775

</biblio>

[[Category:Glycoside Hydrolase Families|GH128]]

Glycoside Hydrolase Family 128

2020-09-29T11:16:17Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
* [[Responsible Curator]]: ^^^Mario Murakami^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH128'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH128.html
|}
</div>


== Substrate specificity and modes of action ==
The first GH128 enzyme, GLU1, was cloned from ''Lentinula edodes'' fruiting bodies (shiitake mushroom) <cite>Sakamoto2011</cite>. GLU1 cleaves β-1,3 linkages in various β-glucans such as endogenous ''L. edodes'' lentinan, laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis'', but does not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. Further work with several GH128 members corroborated that this family is specific for β-1,3-glucans <cite>Santos2020</cite>. Bacterial members from ''Amycolatopsis mediterranei'' (subgroup I) and ''Pseudomonas viridiflava'' (subgroup II)exhibit endo-β-1,3-glucanase activity and catalytic rates notably higher than those observed for fungal members <cite>Santos2020</cite>. On the other hand, fungal members display diverse modes of action and substrate specificity. The GH128 members from ''Aureobsidium namibiae'' (subgroup VI) and ''Cryptococcus neoformans'' (subgroup V) are exo-β-1,3-glucanases and release trisaccharides and monosaccharides from the reducing ends, respectively. The enzyme from ''Blastomyces gilchristii'' (subgroup III) is also an exo-β-1,3-glucanase; however, it releases trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans. The founder member of the family, GLU1 from ''L. edodes'' (subgroup IV) is an endo-β-1,3-glucanase with an atypical mode of substrate recognition as in the subgroup VI. Intriguingly, some fungal members from this family, such as those from ''Trichoderma gamsii'' and ''C. neoformans'', are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) <cite>Santos2020</cite>.

=== Clustering of GH128 ===
[[Image:Santos_GH128_final.png|thumb|right|250px|Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from <cite>Santos2020</cite>.]]
GH128 was created based on the study of ^^^Yuichi Sakamoto^^^ and colleagues <cite>Sakamoto2011</cite>. Years later, a group headed by ^^^Mario Murakami^^^ explored the functional and structural diversity of this family <cite>Santos2020</cite>. For this purpose, they employed phylogenetic and Sequence Similarity Network (SSN, <cite>Atkinson2009</cite>) analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two discrete clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). At least one member of each subgroup was biochemically and structurally characterized. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, feature a substrate-interacting "hydrophobic knuckle" (see [[#Three-dimensional structures]]) and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological functions (nutrition and competition). Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of strategies for substrate recognition (flattening mechanism – subgroups IV and VI; and hydrophobic knuckle – subgroups III, V and VII) and modes of action (exo-enzymes – subgroups III, V and VI; endo-enzymes – subgroup IV; and oligosaccharide binding proteins – subgroup VII).

== Kinetics and Mechanism ==
As indicated by the first study of a GH128 enzyme <cite>Sakamoto2011</cite>, this family is part of [[Clan]] GH-A, thus suggesting that its members operate by a classical Koshland [[retaining]] mechanism. This prediction was confirmed through <sup>1</sup>H-nuclear magnetic resonance spectroscopy of enzymatic products <cite>Santos2020</cite>.

== Catalytic Residues ==
From the sequence alignment of GH128 members, two glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the catalytic residues <cite>Sakamoto2011</cite>. They were further confirmed to be the [[general acid/base]] and the [[catalytic nucleophile]], respectively, by site-directed mutagenesis of the bacterial GH128 member from ''A. mediterranei'' <cite>Santos2020</cite>. These residues are located at the C-terminal ends of the strands β7 and β4 <cite>Santos2020</cite>, as observed for other [[clan]] GH-A families.

== Three-dimensional structures ==
A three-dimensional homology model of ''L. edodes'' GLU1 indicated similarity with several (β/α)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] β-xylosidase and a [[GH5]] β-mannanase <cite>Sakamoto2011</cite>. The fold resembling an (β/α)<sub>8</sub>-barrel was further confirmed with the crystal structure determination of 9 members of the family <cite>Santos2020</cite>. However, in all structures, the helix α2 and the strand β3 are strictly absent <cite>Santos2020</cite>. Moreover, some enzymes such as the endo-β-1,3-glucanase from ''L. edodes'' (GLU1) and the exo-β-1,3-glucanase from ''C. neoformans'', also lack the helices α1 and α3, respectively <cite>Santos2020</cite>.

Two distinct modes of substrate binding were observed in the GH128 family <cite>Santos2020</cite>. The most widespread mode, termed as "hydrophobic knuckle", involves a tryptophan residue that interacts with four glucoside moieties from –5 to –2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties –2 and –3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is referred to as the "flattening" mechanism, due to the unusual, but also stereochemically favorable, conformation adopted by the substrate. It is notable that this mode of substrate binding has not been observed in other CAZy families active on β-1,3-glucans.

== Family Firsts ==
;First stereochemistry determination: predicted to be retaining by membership in Clan GH-A <cite>Sakamoto2011</cite> and further validated by <sup>1</sup>H-NMR of products of the ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First catalytic nucleophile identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First general acid/base residue identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First 3-D structure: predicted by modelling of ''L. edodes'' GLU1 <cite>Sakamoto2011</cite> and experimentally determined for several GH128 members including endo-β-1,3-glucanases from ''A. mediterranei'' (AmGH128_I), ''P. viridiflava'' (PvGH128_II), ''Sorangium cellulosum'' (ScGH128_II) and ''L. edodes'' (LeGH128_IV); exo-β-1,3-glucanases from ''B. gilchristii'' (BgGH128_III), ''C. neoformans'' (CnGH128_V) and ''A. namibiae'' (AnGH128_VI); and β-1,3-glucooligosaccharide binding proteins from ''T. gamsii'' (TgGH128_VII) and ''C. neoformans'' (CnGH128_VII) <cite>Santos2020</cite>.

== References ==
<biblio>

#Sakamoto2011 pmid=21965406
#Santos2020 pmid=32451508
#Atkinson2009 pmid=19190775

</biblio>

[[Category:Glycoside Hydrolase Families|GH128]]

Glycoside Hydrolase Family 128

2020-09-29T11:11:08Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
* [[Responsible Curator]]: ^^^Mario Murakami^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH128'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH128.html
|}
</div>


== Substrate specificity and modes of action ==
The first GH128 enzyme, GLU1, was cloned from ''Lentinula edodes'' fruiting bodies (shiitake mushroom) <cite>Sakamoto2011</cite>. GLU1 cleaves β-1,3 linkages in various β-glucans such as endogenous ''L. edodes'' lentinan, laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis'', but does not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. Further work with several GH128 members corroborated that this family is specific for β-1,3-glucans <cite>Santos2020</cite>. Bacterial members from ''Amycolatopsis mediterranei'' (subgroup I) and ''Pseudomonas viridiflava'' (subgroup II)exhibit endo-β-1,3-glucanase activity and catalytic rates notably higher than those observed for fungal members <cite>Santos2020</cite>. On the other hand, fungal members display diverse modes of action and substrate specificity. The GH128 members from ''Aureobsidium namibiae'' (subgroup VI) and ''Cryptococcus neoformans'' (subgroup V) are exo-β-1,3-glucanases and release trisaccharides and monosaccharides from the reducing ends, respectively. The enzyme from ''Blastomyces gilchristii'' (subgroup III) is also an exo-β-1,3-glucanase; however, it releases trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans. The founder member of the family, GLU1 from ''L. edodes'' (subgroup IV) is an endo-β-1,3-glucanase with an atypical mode of substrate recognition as in the subgroup VI. Intriguingly, some fungal members from this family, such as those from ''Trichoderma gamsii'' and ''C. neoformans'', are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) <cite>Santos2020</cite>.

=== Clustering of GH128 ===
[[Image:Santos_GH128_final.png|thumb|right|250px|Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from <cite>Santos2020</cite>.]]
GH128 was created based on the study of ^^^Yuichi Sakamoto^^^ and colleagues <cite>Sakamoto2011</cite>. Years later, a group headed by ^^^Mario Murakami^^^ explored the functional and structural diversity of this family <cite>Santos2020</cite>. For this purpose, they employed phylogenetic and Sequence Similarity Network (SSN, <cite>Atkinson2009</cite>) analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two discrete clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). At least one member of each subgroup was biochemically and structurally characterized. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, present a substrate-interacting "hydrophobic knuckle" (see [[#Three-dimensional structures]]) and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological function: nutrition and competition. Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of substrate recognition modes (flattening mechanism – subgroups IV and VI; hydrophobic knuckle – subgroups III, V and VII) and mode of action (exo-enzymes – subgroups III, V and VI; endo-enzymes – subgroup IV; oligosaccharide binding proteins – subgroup VII).

== Kinetics and Mechanism ==
As indicated by the first study of a GH128 enzyme <cite>Sakamoto2011</cite>, this family is part of [[Clan]] GH-A, thus suggesting that its members operate by a classical Koshland [[retaining]] mechanism. This prediction was confirmed through <sup>1</sup>H-nuclear magnetic resonance spectroscopy of enzymatic products <cite>Santos2020</cite>.

== Catalytic Residues ==
From the sequence alignment of GH128 members, two glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the catalytic residues <cite>Sakamoto2011</cite>. They were further confirmed to be the [[general acid/base]] and the [[catalytic nucleophile]], respectively, by site-directed mutagenesis of the bacterial GH128 member from ''A. mediterranei'' <cite>Santos2020</cite>. These residues are located at the C-terminal ends of the strands β7 and β4 <cite>Santos2020</cite>, as observed for other [[clan]] GH-A families.

== Three-dimensional structures ==
A three-dimensional homology model of ''L. edodes'' GLU1 indicated similarity with several (β/α)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] β-xylosidase and a [[GH5]] β-mannanase <cite>Sakamoto2011</cite>. The fold resembling an (β/α)<sub>8</sub>-barrel was further confirmed with the crystal structure determination of 9 members of the family <cite>Santos2020</cite>. However, in all structures, the helix α2 and the strand β3 are strictly absent <cite>Santos2020</cite>. Moreover, some enzymes such as the endo-β-1,3-glucanase from ''L. edodes'' (GLU1) and the exo-β-1,3-glucanase from ''C. neoformans'', also lack the helices α1 and α3, respectively <cite>Santos2020</cite>.

Two distinct modes of substrate binding were observed in the GH128 family <cite>Santos2020</cite>. The most widespread mode, termed as "hydrophobic knuckle", involves a tryptophan residue that interacts with four glucoside moieties from –5 to –2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties –2 and –3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is referred to as the "flattening" mechanism, due to the unusual, but also stereochemically favorable, conformation adopted by the substrate. It is notable that this mode of substrate binding has not been observed in other CAZy families active on β-1,3-glucans.

== Family Firsts ==
;First stereochemistry determination: predicted to be retaining by membership in Clan GH-A <cite>Sakamoto2011</cite> and further validated by <sup>1</sup>H-NMR of products of the ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First catalytic nucleophile identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First general acid/base residue identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First 3-D structure: predicted by modelling of ''L. edodes'' GLU1 <cite>Sakamoto2011</cite> and experimentally determined for several GH128 members including endo-β-1,3-glucanases from ''A. mediterranei'' (AmGH128_I), ''P. viridiflava'' (PvGH128_II), ''Sorangium cellulosum'' (ScGH128_II) and ''L. edodes'' (LeGH128_IV); exo-β-1,3-glucanases from ''B. gilchristii'' (BgGH128_III), ''C. neoformans'' (CnGH128_V) and ''A. namibiae'' (AnGH128_VI); and β-1,3-glucooligosaccharide binding proteins from ''T. gamsii'' (TgGH128_VII) and ''C. neoformans'' (CnGH128_VII) <cite>Santos2020</cite>.

== References ==
<biblio>

#Sakamoto2011 pmid=21965406
#Santos2020 pmid=32451508
#Atkinson2009 pmid=19190775

</biblio>

[[Category:Glycoside Hydrolase Families|GH128]]

Glycoside Hydrolase Family 128

2020-09-29T11:04:54Z

Mario Murakami:

{{UnderConstruction}}
* [[Author]]: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
* [[Responsible Curator]]: ^^^Mario Murakami^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH128'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH128.html
|}
</div>


== Substrate specificities ==
The first GH128 enzyme, GLU1, was cloned from ''Lentinula edodes'' fruiting bodies (shiitake mushroom) <cite>Sakamoto2011</cite>. GLU1 cleaves β-1,3 linkages in various β-glucans such as endogenous ''L. edodes'' lentinan, laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis'', but does not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. Further work with several GH128 members corroborated that this family is specific for β-1,3-glucans <cite>Santos2020</cite>. Bacterial members from ''Amycolatopsis mediterranei'' (subgroup I) and ''Pseudomonas viridiflava'' (subgroup II)exhibit endo-β-1,3-glucanase activity and catalytic rates notably higher than those observed for fungal members <cite>Santos2020</cite>. On the other hand, fungal members display diverse modes of action and substrate specificity. The GH128 members from ''Aureobsidium namibiae'' (subgroup VI) and ''Cryptococcus neoformans'' (subgroup V) are exo-β-1,3-glucanases and release trisaccharides and monosaccharides from the reducing ends, respectively. The enzyme from ''Blastomyces gilchristii'' (subgroup III) is also an exo-β-1,3-glucanase; however, it releases trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans. The founder member of the family, GLU1 from ''L. edodes'' (subgroup IV) is an endo-β-1,3-glucanase with an atypical mode of substrate recognition as in the subgroup VI. Intriguingly, some fungal members from this family, such as those from ''Trichoderma gamsii'' and ''C. neoformans'', are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) <cite>Santos2020</cite>.

=== Clustering of GH128 ===
[[Image:Santos_GH128_final.png|thumb|right|250px|Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from <cite>Santos2020</cite>.]]
GH128 was created based on the study of ^^^Yuichi Sakamoto^^^ and colleagues <cite>Sakamoto2011</cite>. Years later, a group headed by ^^^Mario Murakami^^^ explored the functional and structural diversity of this family <cite>Santos2020</cite>. For this purpose, they employed phylogenetic and Sequence Similarity Network (SSN, <cite>Atkinson2009</cite>) analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two discrete clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). At least one member of each subgroup was biochemically and structurally characterized: AmGH128_I, PvGH128_II, ScGH128_II, BgGH128_III, LeGH128_IV, CnGH128_V, AnGH128_VI, TgGH128_VII and CnGH128_VII. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, present a substrate-interacting "hydrophobic knuckle" (see [[#Three-dimensional structures]]) and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological function: nutrition and competition. Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of substrate recognition modes (flattening mechanism – subgroups IV and VI; hydrophobic knuckle – subgroups III, V and VII) and mode of action (exo-enzymes – subgroups III, V and VI; endo-enzymes – subgroup IV; oligosaccharide binding proteins – subgroup VII).

== Kinetics and Mechanism ==
As indicated by the first study of a GH128 enzyme <cite>Sakamoto2011</cite>, this family is part of [[Clan]] GH-A, thus suggesting that its members operate by a classical Koshland [[retaining]] mechanism. This prediction was confirmed through <sup>1</sup>H-nuclear magnetic resonance spectroscopy of enzymatic products <cite>Santos2020</cite>.

== Catalytic Residues ==
From the sequence alignment of GH128 members, two glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the catalytic residues <cite>Sakamoto2011</cite>. They were further confirmed to be the [[general acid/base]] and the [[catalytic nucleophile]], respectively, by site-directed mutagenesis of the bacterial GH128 member from ''A. mediterranei'' <cite>Santos2020</cite>. These residues are located at the C-terminal ends of the strands β7 and β4 <cite>Santos2020</cite>, as observed for other [[clan]] GH-A families.

== Three-dimensional structures ==
A three-dimensional homology model of ''L. edodes'' GLU1 indicated similarity with several (β/α)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] β-xylosidase and a [[GH5]] β-mannanase <cite>Sakamoto2011</cite>. The fold resembling an (β/α)<sub>8</sub>-barrel was further confirmed with the crystal structure determination of 9 members of the family <cite>Santos2020</cite>. However, in all structures, the helix α2 and the strand β3 are strictly absent <cite>Santos2020</cite>. Moreover, some enzymes such as the endo-β-1,3-glucanase from ''L. edodes'' (GLU1) and the exo-β-1,3-glucanase from ''C. neoformans'', also lack the helices α1 and α3, respectively <cite>Santos2020</cite>.

Two distinct modes of substrate binding were observed in the GH128 family <cite>Santos2020</cite>. The most widespread mode, termed the "hydrophobic knuckle", involves a tryptophan residue that interacts with four glucoside moieties from –5 to –2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties –2 and –3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is referred to as the "flattening" mechanism, due to the unusual, but also stereochemically favorable, conformation adopted by the substrate. It is notable that the mode of substrate binding has not been observed in other CAZy families active on β-1,3-glucans.

== Family Firsts ==
;First stereochemistry determination: predicted to be retaining by membership in Clan GH-A <cite>Sakamoto2011</cite> and further validated by <sup>1</sup>H-NMR of products of the ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First catalytic nucleophile identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First general acid/base residue identification: predicted by sequence alignment <cite>Sakamoto2011</cite> and confirmed by site-directed mutagenesis of ''A. mediterranei'' endo-β-1,3-glucanase (AmGH128_I) <cite>Santos2020</cite>.
;First 3-D structure: predicted by modelling of ''L. edodes'' GLU1 <cite>Sakamoto2011</cite> and experimentally determined for several GH128 members including endo-β-1,3-glucanases from ''A. mediterranei'' (AmGH128_I), ''P. viridiflava'' (PvGH128_II), ''Sorangium cellulosum'' (ScGH128_II) and ''L. edodes'' (LeGH128_IV); exo-β-1,3-glucanases from ''B. gilchristii'' (BgGH128_III), ''C. neoformans'' (CnGH128_V) and ''A. namibiae'' (AnGH128_VI); and β-1,3-glucooligosaccharide binding proteins from ''T. gamsii'' (TgGH128_VII) and ''C. neoformans'' (CnGH128_VII) <cite>Santos2020</cite>.

== References ==
<biblio>

#Sakamoto2011 pmid=21965406
#Santos2020 pmid=32451508
#Atkinson2009 pmid=19190775

</biblio>

[[Category:Glycoside Hydrolase Families|GH128]]

User:Mario Murakami

2020-06-22T13:10:10Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production <cite>Fonseca2020</cite>. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)

[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose

[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose

[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant

[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)

[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose

[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)

[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)

[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose

[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)

[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 crystal form)

[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 crystal form)

[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose

[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)

[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)

[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose

[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site

[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)

[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - BlMan5B, E257A mutant

[{{PDBlink}}6MP7 PDB ID 6MP7] - BlMan5B, E257A mutant, in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - BlMan5B, E257A mutant, in complex with GlcNAc (co-crystallization)

[{{PDBlink}}4W7U PDB ID 4W7U] - Xac0030, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W7V PDB ID 4W7V] - Xac0030 in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - Xac0030 in complex with cellopentaose

[{{PDBlink}}5HNN PDB ID 5HNN] - Xac0030, triple mutation H174W, Y211A and K227R

[{{PDBlink}}5HOS PDB ID 5HOS] - Xac0029, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - A GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-mannanase from ''Thermotoga petrophila'' RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan5A in complex with glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from ''Bacillus subtilis'' 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - ThBgl, a GH1 beta-glucosidase from ''Trichoderma harzianum''

[{{PDBlink}}6EFU PDB ID 6EFU] - ThBgl, double mutant L167W/P172L

[{{PDBlink}}5WKA PDB ID 5WKA] - a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - EaBgl, GH1 beta-glucosidase from ''Exiguobacterium antarcticum'' B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - EaBgl (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - HiBG, a GH1 beta-glucosidase from the fungus ''Humicola insolens''

[{{PDBlink}}4MDP PDB ID 4MDP] - HiBG in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from ''Bacillus licheniformis''

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S)

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from ''Thermotoga petrophila'' RKU-1

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - XacMan2A, nucleophile mutant (E575A)

[{{PDBlink}}6BYI PDB ID 6BYI] - XacMan2A, Acid/Base mutant (E477A)

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon ''Thermococcus kodakaraensis''

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - XacAbf51, a GH51 arabinofuranosidase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from ''Thermotoga petrophila'' RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - BbgII, a GH42 beta-galactosidase from ''Bifidobacterium bifidum''

[{{PDBlink}}4UCF PDB ID 4UCF] - BbgII in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from ''Caulobacter crescentus''

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - Endo-beta-1,3-1,4 glucanase from ''Bacillus subtilis'' (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - A GH8 endo-beta-1,4-glucanase from an ''Achatina fulica'' gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - A GH12 Xyloglucanase from ''Aspergillus niveus''

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - A GH11 xylanase A from ''Bacillus subtilis'' 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - KpLPMO10A, a AA10 LPMO from ''Kitasatospora papulosa''

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from ''Bacillus subtilis''

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T13:07:44Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production <cite>Fonseca2020</cite>. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)

[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose

[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose

[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant

[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)

[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose

[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)

[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)

[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose

[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)

[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 crystal form)

[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 crystal form)

[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose

[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)

[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)

[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose

[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site

[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)

[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - BlMan5B, E257A mutant

[{{PDBlink}}6MP7 PDB ID 6MP7] - BlMan5B, E257A mutant, in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - BlMan5B, E257A mutant, in complex with GlcNAc (co-crystallization)

[{{PDBlink}}4W7U PDB ID 4W7U] - Xac0030, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W7V PDB ID 4W7V] - Xac0030 in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - Xac0030 in complex with cellopentaose

[{{PDBlink}}5HNN PDB ID 5HNN] - Xac0030, triple mutation H174W, Y211A and K227R

[{{PDBlink}}5HOS PDB ID 5HOS] - Xac0029, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - A GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-mannanase from ''Thermotoga petrophila'' RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan5A in complex with glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from ''Bacillus subtilis'' 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - ThBgl, a GH1 beta-glucosidase from ''Trichoderma harzianum''

[{{PDBlink}}6EFU PDB ID 6EFU] - ThBgl, double mutant L167W/P172L

[{{PDBlink}}5WKA PDB ID 5WKA] - a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - EaBgl, GH1 beta-glucosidase from ''Exiguobacterium antarcticum'' B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - EaBgl (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - HiBG, a GH1 beta-glucosidase from the fungus ''Humicola insolens''

[{{PDBlink}}4MDP PDB ID 4MDP] - HiBG in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from ''Bacillus licheniformis''

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S)

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from ''Thermotoga petrophila'' RKU-1

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - XacMan2A, nucleophile mutant (E575A)

[{{PDBlink}}6BYI PDB ID 6BYI] - XacMan2A, Acid/Base mutant (E477A)

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon ''Thermococcus kodakaraensis''

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - XacAbf51, a GH51 arabinofuranosidase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from ''Thermotoga petrophila'' RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - BbgII, a GH42 beta-galactosidase from ''Bifidobacterium bifidum''

[{{PDBlink}}4UCF PDB ID 4UCF] - BbgII in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from ''Caulobacter crescentus''

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - Endo-beta-1,3-1,4 glucanase from ''Bacillus subtilis'' (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - A GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - A GH12 Xyloglucanase from ''Aspergillus niveus''

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - A GH11 xylanase A from ''Bacillus subtilis'' 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - KpLPMO10A, a AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T13:05:26Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)

[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose

[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose

[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant

[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)

[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose

[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)

[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)

[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose

[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)

[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 crystal form)

[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 crystal form)

[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose

[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)

[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)

[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose

[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site

[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)

[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - BlMan5B, E257A mutant

[{{PDBlink}}6MP7 PDB ID 6MP7] - BlMan5B, E257A mutant, in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - BlMan5B, E257A mutant, in complex with GlcNAc (co-crystallization)

[{{PDBlink}}4W7U PDB ID 4W7U] - Xac0030, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W7V PDB ID 4W7V] - Xac0030 in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - Xac0030 in complex with cellopentaose

[{{PDBlink}}5HNN PDB ID 5HNN] - Xac0030, triple mutation H174W, Y211A and K227R

[{{PDBlink}}5HOS PDB ID 5HOS] - Xac0029, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - A GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-mannanase from ''Thermotoga petrophila'' RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan5A in complex with glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from ''Bacillus subtilis'' 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - ThBgl, a GH1 beta-glucosidase from ''Trichoderma harzianum''

[{{PDBlink}}6EFU PDB ID 6EFU] - ThBgl, double mutant L167W/P172L

[{{PDBlink}}5WKA PDB ID 5WKA] - a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - EaBgl, GH1 beta-glucosidase from ''Exiguobacterium antarcticum'' B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - EaBgl (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - HiBG, a GH1 beta-glucosidase from the fungus ''Humicola insolens''

[{{PDBlink}}4MDP PDB ID 4MDP] - HiBG in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from ''Bacillus licheniformis''

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S)

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from ''Thermotoga petrophila'' RKU-1

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - XacMan2A, nucleophile mutant (E575A)

[{{PDBlink}}6BYI PDB ID 6BYI] - XacMan2A, Acid/Base mutant (E477A)

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon ''Thermococcus kodakaraensis''

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - XacAbf51, a GH51 arabinofuranosidase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from ''Thermotoga petrophila'' RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - BbgII, a GH42 beta-galactosidase from ''Bifidobacterium bifidum''

[{{PDBlink}}4UCF PDB ID 4UCF] - BbgII in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from ''Caulobacter crescentus''

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - Endo-beta-1,3-1,4 glucanase from ''Bacillus subtilis'' (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - A GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - A GH12 Xyloglucanase from ''Aspergillus niveus''

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - A GH11 xylanase A from ''Bacillus subtilis'' 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - KpLPMO10A, a AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T11:33:49Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)

[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose

[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose

[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant

[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)

[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose

[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)

[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)

[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose

[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)

[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 crystal form)

[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 crystal form)

[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose

[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)

[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)

[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose

[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site

[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)

[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - BlMan5B, E257A mutant

[{{PDBlink}}6MP7 PDB ID 6MP7] - BlMan5B, E257A mutant, in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - BlMan5B, E257A mutant, in complex with GlcNAc (co-crystallization)

[{{PDBlink}}4W7U PDB ID 4W7U] - Xac0030, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W7V PDB ID 4W7V] - Xac0030 in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - Xac0030 in complex with cellopentaose

[{{PDBlink}}5HNN PDB ID 5HNN] - Xac0030, triple mutation H174W, Y211A and K227R

[{{PDBlink}}5HOS PDB ID 5HOS] - Xac0029, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - A GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-mannanase from ''Thermotoga petrophila'' RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan5A in complex with glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T11:14:08Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)

[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose

[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose

[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant

[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)

[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose

[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)

[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)

[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose

[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)

[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose

[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)

[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)

[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose

[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site

[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)

[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase (Xac0029) from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T11:13:23Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)

[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant

[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)

[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose

[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)

[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)

[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose

[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)

[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose

[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)

[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)

[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose

[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site

[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)

[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase (Xac0029) from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T01:04:16Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase (Xac0029) from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T01:03:43Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-22T00:17:39Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structural and functional studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-21T01:34:20Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-21T01:33:29Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:41:32Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:40:54Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:36:33Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:32:42Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:32:01Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of coagulation cascade and mechanochemical enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:28:40Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH39'''

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:25:36Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

GH57
[{{PDBlink}}3N8T PDB ID 3N8T] - Native TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose

GH22

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

GH51

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

GH42

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase
[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

GH16

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

GH26
[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

GH8

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

GH12
[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

GH39
[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

CBM3
[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

GH11
[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

AA10

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:22:30Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

GH43

[{{PDBlink}}6MS3 PDB ID 6MS3] - GH43 protein BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}6MS2 PDB ID 6MS2] - GH43 BlXynB protein from Bacillus licheniformis
[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

GH2
[{{PDBlink}}6BYE PDB ID 6BYE] - GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri in complex with mannose
[{{PDBlink}}6BYG PDB ID 6BYG] - nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri
[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYC PDB ID 6BYC] - GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

GH57
[{{PDBlink}}3N8T PDB ID 3N8T] - Native TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose

GH22

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

GH51

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

GH42

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase
[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

GH16

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

GH26
[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

GH8

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

GH12
[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

GH39
[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

CBM3
[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

GH11
[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

AA10

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T23:21:34Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

GH1
[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W / P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

GH43

[{{PDBlink}}6MS3 PDB ID 6MS3] - GH43 protein BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}6MS2 PDB ID 6MS2] - GH43 BlXynB protein from Bacillus licheniformis
[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

GH2
[{{PDBlink}}6BYE PDB ID 6BYE] - GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri in complex with mannose
[{{PDBlink}}6BYG PDB ID 6BYG] - nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri
[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYC PDB ID 6BYC] - GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

GH57
[{{PDBlink}}3N8T PDB ID 3N8T] - Native TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose

GH22

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

[{{PDBlink}}6B7W PDB ID 6B7W] - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

GH51

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

GH42

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase
[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

GH16

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

GH26
[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

GH8

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

GH12
[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

GH39
[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

CBM3
[{{PDBlink}}2L8A PDB ID 2L8A] – a CBM3 lacking the calcium-binding site from Bacillus subtilis

GH11
[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

AA10

[{{PDBlink}}6NDQ PDB ID 6NDQ] – an AA10 LPMO from Kitasatospora papulosa

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T22:55:46Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T22:55:03Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2014a</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2015</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T22:53:06Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2015</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T22:52:14Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2015</cite>, the mechanistic understanding and rational design of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

GH5

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T22:06:41Z

Mario Murakami:

[[Image:Murakami.jpg|250px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013, Furtado2015</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2015</cite>, the mechanistic understanding and rational design of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014</cite>.

----

'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

[{{PDBlink}}6UAS PDB ID 6UAS] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UAR PDB ID 6UAR] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

[{{PDBlink}}6UAU PDB ID 6UAU] - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

[{{PDBlink}}6UAT PDB ID 6UAT] - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

[{{PDBlink}}6UFZ PDB ID 6UFZ] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

[{{PDBlink}}6UFL PDB ID 6UFL] - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

[{{PDBlink}}6UAW PDB ID 6UAW] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 PDB ID 6UB0] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

[{{PDBlink}}6UNV PDB ID 6UNV] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

[{{PDBlink}}6UAY PDB ID 6UAY] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

[{{PDBlink}}6UB1 PDB ID 6UB1] - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

[{{PDBlink}}6UB4 PDB ID 6UB4] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

[{{PDBlink}}6UB3 PDB ID 6UB3] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

[{{PDBlink}}6UB6 PDB ID 6UB6] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

[{{PDBlink}}6UB5 PDB ID 6UB5] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

[{{PDBlink}}6UBB PDB ID 6UBB] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

[{{PDBlink}}6UBA PDB ID 6UBA] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

GH5
[{{PDBlink}}6MP2 PDB ID 6MP2] - GH5 BlMan5B solved by SIRAS

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

[{{PDBlink}}5HNN PDB ID 5HNN] - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

[{{PDBlink}}5HOS PDB ID 5HOS] – GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}5HPC PDB ID 5HPC] – GH5 XacCel5A crystallized in the space group P41212

[{{PDBlink}}4W7U PDB ID 4W7U] – GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] – GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in the native form

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in the native form

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in complex with XXLG

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library in complex with cellotriose

[{{PDBlink}}4M1R PDB ID 4M1R] GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1

[{{PDBlink}}3PZM PDB ID 3PZM] - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with maltose and glycerol

[{{PDBlink}}3PZG PDB ID 3PZG] - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (I222 crystal form)

[{{PDBlink}}3PZI PDB ID 3PZI] - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with beta-D-glucose

[{{PDBlink}}3PZU PDB ID 3PZU] – GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

[{{PDBlink}}3PZV PDB ID 3PZV] – GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] – GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 with manganese(II) ion

----

'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322
#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-20T22:04:11Z

Mario Murakami:

User:Mario Murakami

2020-06-20T15:12:08Z

Mario Murakami:

User:Mario Murakami

2020-06-20T11:40:49Z

Mario Murakami:

User:Mario Murakami

2020-06-20T10:50:07Z

Mario Murakami:

User:Mario Murakami

2020-06-18T23:15:20Z

Mario Murakami:

User:Mario Murakami

2020-06-18T23:09:55Z

Mario Murakami:

User:Mario Murakami

2020-06-18T19:02:17Z

Mario Murakami:

User:Mario Murakami

2020-06-18T19:02:03Z

Mario Murakami:

[[Image:Murakami.jpg|200px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2012, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Diogo2015, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite>and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

----

Selected publications

Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, and Murakami MT. (2020) Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol. DOI:10.1038/s41589-020-0554-5 [http://www.hubmed.org/display.cgi?uids=32451508 HubMed]

Fonseca LM, Parreiras LS, and Murakami MT. (2020) Rational engineering of the Trichoderma reesei RUT-C30 strain into an industrially relevant platform for cellulase production. Biotechnol Biofuels. 13, 93. DOI:10.1186/s13068-020-01732-w [http://www.hubmed.org/display.cgi?uids=32461765 HubMed]

Corrêa TLR, Júnior AT, Wolf LD, Buckeridge MS, Dos Santos LV, and Murakami MT. (2019) An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification. Biotechnol Biofuels. 12, 117. DOI:10.1186/s13068-019-1449-0 [http://www.hubmed.org/display.cgi?uids=31168322 HubMed]

----

Crystal structures

----

List of publications
<biblio>

#Giuseppe2012 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Diogo2015 pmid=25640722
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322

#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-18T19:01:43Z

Mario Murakami:

[[Image:Murakami.jpg|300px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2012, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Diogo2015, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite>and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

----

Selected publications

Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, and Murakami MT. (2020) Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol. DOI:10.1038/s41589-020-0554-5 [http://www.hubmed.org/display.cgi?uids=32451508 HubMed]

Fonseca LM, Parreiras LS, and Murakami MT. (2020) Rational engineering of the Trichoderma reesei RUT-C30 strain into an industrially relevant platform for cellulase production. Biotechnol Biofuels. 13, 93. DOI:10.1186/s13068-020-01732-w [http://www.hubmed.org/display.cgi?uids=32461765 HubMed]

Corrêa TLR, Júnior AT, Wolf LD, Buckeridge MS, Dos Santos LV, and Murakami MT. (2019) An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification. Biotechnol Biofuels. 12, 117. DOI:10.1186/s13068-019-1449-0 [http://www.hubmed.org/display.cgi?uids=31168322 HubMed]

----

Crystal structures

----

List of publications
<biblio>

#Giuseppe2012 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Diogo2015 pmid=25640722
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322

#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-18T11:51:19Z

Mario Murakami:

[[Image:Murakami.jpg|300px|right]]

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families [[GH1]] <cite>Giuseppe2012, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Diogo2015, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite>and [[AA9]] <cite>Correa2019</cite>. Recently, his group rationally engineered a publicly available strain (''Trichoderma reesei'' RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess <cite>Fonseca2020</cite>.

----

References
<biblio>

#Giuseppe2012 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Diogo2015 pmid=25640722
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322

#Fonseca2020 pmid=32461765

</biblio>


[[Category:Contributors|Murakami,Mario]]

User:Mario Murakami

2020-06-18T02:07:05Z

Mario Murakami:

User:Mario Murakami

2020-06-18T02:06:27Z

Mario Murakami: