CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 89

2023-07-06T10:21:52Z

Mariana Morais:

{{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]], no catalytic activity of the isolated CapCBM89 was observed on the substrates tested <cite>Cabral2022</cite>.

== Structural Features ==

[[File:Cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure (PDB 7JVI [https://www.rcsb.org/structure/7JVI]). The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
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>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 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 ==

In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The most common associated glycoside hydrolases are from the [[GH10]] family. 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 for catalysis <cite>Cabral2022</cite>.

== 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 [{{PDBlink}}7jvi PDB 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

2023-07-06T10:18:30Z

Mariana Morais:

{{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]], no catalytic activity of the isolated CapCBM89 was observed on the substrates tested <cite>Cabral2022</cite>.

== Structural Features ==

[[File:Cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure. The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
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>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 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 ==

In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The most common associated glycoside hydrolases are from the [[GH10]] family. 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 for catalysis <cite>Cabral2022</cite>.

== 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 [{{PDBlink}}7jvi PDB 7JVI], retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .

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

</biblio>


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

File:Cbm89 cazypedia.png

2023-07-06T10:18:03Z

Mariana Morais:

Carbohydrate Binding Module Family 89

2023-07-06T10:16:35Z

Mariana Morais:

{{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]], no catalytic activity of the isolated CapCBM89 was observed on the substrates tested <cite>Cabral2022</cite>.

== Structural Features ==

[[File:cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure. The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
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>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 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 ==

In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The most common associated glycoside hydrolases are from the [[GH10]] family. 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 for catalysis <cite>Cabral2022</cite>.

== 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 [{{PDBlink}}7jvi PDB 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

2023-06-21T14:52:58Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral2022</cite> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 putative region for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <cite>Cabral2022</cite> . The 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, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <cite>Cabral2022</cite>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
*'''First Identified:''' The first CBM89 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]]

Carbohydrate Binding Module Family 89

2023-06-21T14:50:53Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral2022</cite> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 putative region for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <cite>Cabral2022</cite> . The 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, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <cite>Cabral2022</cite>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
'''First Identified'''
The first CBM89 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]]

Carbohydrate Binding Module Family 89

2023-06-21T14:49:57Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral2022</cite> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 Ca2+ 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 putative region for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <cite>Cabral2022</cite> . The 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, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <cite>Cabral2022</cite>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
'''First Identified'''
The first CBM89 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]]

Carbohydrate Binding Module Family 89

2023-06-21T14:47:06Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <ref>Cabral2022</ref>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <ref>Cabral2022</ref>.

== Structural Features ==

* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <ref>Cabral2022</ref> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <ref>Cabral2022</ref>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding <ref>Cabral2022</ref> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <ref>Cabral2022</ref> . The cluster encodes the CapCBM89-GH10 and two exo-acting enzymes from GH43 and GH97 families <ref>Cabral2022</ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <ref>Cabral2022</ref>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
'''First Identified'''
The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <ref>Cabral2022</ref> .
'''First Structural Characterization'''
The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <ref>Cabral2022</ref> .

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

</biblio>


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

Carbohydrate Binding Module Family 89

2023-06-21T14:45:54Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <ref>Cabral2022</ref>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <ref>Cabral2022</ref>.

== Structural Features ==

* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <ref>Cabral2022</ref> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <ref>Cabral2022</ref>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding <ref>Cabral2022</ref> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <ref>Cabral2022</ref> . The cluster encodes the CapCBM89-GH10 and two exo-acting enzymes from GH43 and GH97 families <ref>Cabral2022</ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <ref>Cabral2022</ref>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
''';First Identified'''
The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <ref>Cabral2022</ref> .
''';First Structural Characterization'''
The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <ref>Cabral2022</ref> .

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

</biblio>


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

Carbohydrate Binding Module Family 89

2023-06-21T14:38:43Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <cite>Cabral202Cabral202<cite>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <cite>Cabral202Cabral202<cite>.

== Structural Features ==
''Content in this section should include, in paragraph form, a description of:''
* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral2022<cite> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral202Cabral2022<cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding <cite>Cabral2022<cite>.

== Functionalities ==
''Content in this section should include, in paragraph form, a description of:''
* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <cite>Cabral202Cabral202<cite>. The cluster encodes the CapCBM89-GH10 and two exo-enzymes from GH43 and GH97 families <ref>Cabral2022<ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <cite>Cabral202Cabral202<cite>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
''';First Identified'''
The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <cite>Cabral202Cabral202<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>Cabral202Cabral202<cite>.

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

</biblio>


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

Carbohydrate Binding Module Family 89

2023-06-21T14:34:51Z

Mariana Morais:

{{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 ==
CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <cite>Cabral202Cabral202<cite>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <cite>Cabral202Cabral202<cite>.

== Structural Features ==
''Content in this section should include, in paragraph form, a description of:''
* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral202Cabral202<cite> displays a parallel β-helix fold, consisting of 14 complete helical turns.

* '''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> 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 Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral202Cabral202<cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding <cite>Cabral202Cabral202<cite>.

== Functionalities ==
''Content in this section should include, in paragraph form, a description of:''
* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <cite>Cabral202Cabral202<cite>. The cluster encodes the CapCBM89-GH10 and two exo-enzymes from GH43 and GH97 families <ref>Cabral2022<ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <cite>Cabral202Cabral202<cite>.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.

== Family Firsts ==
;First Identified The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <cite>Cabral202Cabral202<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>Cabral202Cabral202<cite>.

== References ==
<biblio>
#Cabral20222 pmid= 35110564

</biblio>


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

User:Mariana Morais

2023-03-27T20:00:38Z

Mariana Morais:

[[File:Picture mmorais.jpg|thumb]]

'''Mariana Abrahão Bueno de Morais''' is a researcher in the Brazilian Biorenewables National Laboratory [https://lnbr.cnpem.br/en/ (LNBR)] from the Brazilian Center for Research in Energy and Materials [https://cnpem.br/en/ (CNPEM)]. She has been focused on the elucidation of enzymes molecular mechanisms, integrating experimental data with computational approaches, including molecular modeling, classical and Quantum Mechanics simulations.
She obtained a degree in Biotechnology Engineering at the São Paulo State University and her PhD (emphasis in Biochemistry) at the State University of Campinas, developing the project at CNPEM (Brazil) under the supervision of [[User:Mario_Murakami|Mario Murakami]], with a period at the IBMC/[https://www.i3s.up.pt/ I3S] Institute (Portugal) under the supervision of Prof. Ana Tomas. Mariana did a postdoc at the University of Barcelona in the group of Prof. Carme Rovira ([https://sites.google.com/site/roviralab/ QSBio]), working with hybrid QM/MM simulations.

<br>
Mariana has contributed to studies related to members of the following CAZy families: <br>
'''[[Glycoside_Hydrolase_Family_1|GH1]]''' <cite>Santos2019,Sousa2020,Toyama2018</cite>, '''[[Glycoside_Hydrolase_Family_2|GH2]]''' <cite>Domingues2018</cite>, '''[[Glycoside_Hydrolase_Family_5|GH5]]''' subfamily 57 <cite>Martins2022</cite>, '''[[Glycoside_Hydrolase_Family_26|GH26]]''' <cite>Mandelli2020</cite>, '''[[Glycoside_Hydrolase_Family_38|GH38]]''' <cite>Cordeiro2023</cite>, '''[[Glycoside_Hydrolase_Family_39|GH39]]''' <cite>Morais2020</cite>, '''[[Glycoside_Hydrolase_Family_43|GH43]]''' <cite>Morais2021,Zanphorlin2019,Vieira2021</cite>, '''[[Glycoside_Hydrolase_Family_51|GH51]]''' <cite>Santos2018</cite>, '''[[Glycoside_Hydrolase_Family_173|GH173]]''' <cite>Cabral2022</cite>, '''[[Carbohydrate_Binding_Module_Family_3|CBM3]]''' <cite>Morais2023</cite>, '''[https://cazypedia.msl.ubc.ca/index.php/Carbohydrate_Binding_Module_Family_89 CBM89]''' <cite>Cabral2022</cite>.

Structures on Protein Data Bank (PDB):
<br>
'''GH1''':
PDB ID [https://www.rcsb.org/structure/6efu 6EFU] (ThBgl double mutant, a tailored beta-glucosidase from ''Trichoderma harzianum''); PDB ID [https://www.rcsb.org/structure/6WIU 6WIU] (EmBgl, a beta-glucosidase from the marine bacterium ''Exiguobacterium marinum''); PDB ID [https://www.rcsb.org/structure/5WKA 5WKA] (AmBgl-LP, a beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake). <br>
'''GH2''':PDB ID [https://www.rcsb.org/structure/6BYC 6BYC] (XacMan2A, an exo-beta-mannanase from ''Xanthomonas axonopodis'' pv. citri); PDB ID [https://www.rcsb.org/structure/6BYE 6BYE] (XacMan2A, in complex with mannose); PDB ID [https://www.rcsb.org/structure/6BYG 6BYG] (XacMan2A, nucleophile mutant); PDB ID [https://www.rcsb.org/structure/6BYI 6BYI] (XacMan2A, acid/base mutant).<br>
'''GH5''': PDB ID [https://www.rcsb.org/structure/8D89 8D89] (CapGH5_57, '''first structure of subfamily 57''', from an uncultured ''Bacteroidales bacterium'' recovered from the capybara gut microbiota). <br>
'''GH26''':
PDB ID [https://www.rcsb.org/structure/6UEH 6UEH] (Ruminal GH26 endo-beta-1,4-mannanase). <br>
'''GH39''': PDB ID [https://www.rcsb.org/structure/6UQJ 6UQJ] (XacGH39, beta-xylasidase from ''Xanthomonas axonopodis'' pv. citri). <br>
'''GH43''': PDB ID [https://www.rcsb.org/structure/6MS2 6MS2] (BlXynB, an inactive GH43 member from ''Bacillus licheniformis''); PDB ID [https://www.rcsb.org/structure/6MS3 6MS3 (Active BlXynB mutant (K247S)); PDB ID [https://www.rcsb.org/structure/6XN0 6XN0] (XacGH43_1, calcium activated exo-oligoxylanase from Xanthomonas citri); PDB ID [https://www.rcsb.org/structure/6XN1 6XN1] (XacGH43_1 complexed with xylose (Michaelis complex <cite>Morais2021</cite>)); PDB ID [https://www.rcsb.org/structure/6XN2 6XN2] (XacGH43_1 complexed with xylotriose); PDB ID [https://www.rcsb.org/structure/7JVH 7JVH] (GH43_12 retrieved from capybara gut metagenome). <br>
'''GH51''': PDB ID [https://www.rcsb.org/structure/6D25 6D25] (XacAbf51, arabinofuranosidase that recognize arabinofuranosyl di-substitutions). <br>
'''CBM3''': PDB ID [https://www.rcsb.org/structure/6UFV 6UFV] (BsCBM3, CBM3 from ''Bacillus subtilis'' at 1.28 angstrom resolution); PDB ID [https://www.rcsb.org/structure/6UFW 6UFW] (BsCBM3, CBM3 from ''Bacillus subtilis'' at 1.06 angstrom resolution). <br>
'''CBM89''': PDB ID [https://www.rcsb.org/structure/7JVI 7JVI] (CapCBM89, '''first structure of CBM89 family''', retrieved from capybara gut metagenome).
----

<biblio>
#Santos2019 pmid=30894609
#Sousa2020 <div>[https://doi.org/10.1002/bbb.2136 https://doi.org/10.1002/bbb.2136]</div>
#Toyama2018 pmid=29454992
#Domingues2018 pmid=29997257
#Martins2022 pmid=36322419
#Mandelli2020 pmid=32139511
#Cordeiro2023 pmid=36443572
#Morais2020 pmid=32500063
#Morais2021 pmid=33446650
#Zanphorlin2019 pmid=30556897
#Santos2018 pmid=30127853
#Cabral2022 pmid=35110564
#Morais2023 pmid=36680939
#Vieira2021 pmid=34193873

</biblio>


[[Category:Contributors|Morais,Mariana]]

File:Picture mmorais.jpg

2023-03-27T18:45:36Z

Mariana Morais:

picture