Glycoside Hydrolase Family 151

2020-06-04T10:17:18Z

David Teze:

{{UnderConstruction}}
* [[Author]]: ^^^Casper Wilkens^^^, ^^^David Teze^^^, and ^^^Birgitte Zeuner^^^
* [[Responsible Curator]]: ^^^Birgitte Zeuner^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH151'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Retaining (inferred)
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH151.html
|}
</div>


== Substrate specificities ==
Members of [[GH151]] are bacterial enzymes presenting α-L-fucosidase activity (EC 3.2.1.51) <cite>Sela2012 Benesova2015 Lezyk2016</cite>. Activity has been observed on 4-nitrophenyl-α-L-fucopyranoside (''p''NP-α-L-Fuc) <cite>Benesova2015 Lezyk2016</cite> and on 2-chloro-4-nitrophenyl-α-L-fucopyranoside (CNP-α-L-Fuc) <cite>Sela2012</cite>. GH151 α-L-fucosidases are reportedly unable to catalyze hydrolysis of human milk oligosaccharide structures 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL) <cite>Sela2012 Lezyk2016</cite>, but slight activity has been observed on the blood group H antigen disaccharide Fuc-α-1,2-Gal <cite>Sela2012</cite>. No activity was observed on fucosylated xyloglucan <cite>Lezyk2016</cite>.

The first characterized members of GH151 were perceived as members of [[GH29]] due to their α-L-fucosidase activity <cite>Sela2012 Lezyk2016</cite>. However, phylogenetic analysis and sequence alignment revealed poor homology to GH29 <cite>Sela2012 Lezyk2016</cite>. Based on the low sequence similarity to GH29, it was suggested that a new GH family be created <cite>Benesova2015</cite>. Sequence homology to β-galactosidase trimerization domains has been reported <cite>Sela2012 Lezyk2016</cite>. Consequently, one GH151 α-L-fucosidase was tested for activity on pNP-β-D-Gal, ''p''NP-β-D-Glc, and ''p''NP-β-D-Lac, but none was observed <cite>Lezyk2016</cite>.

== Kinetics and Mechanism ==

The catalytic mechanism of GH151 has not been determined, but based on reports that two members of GH151 can catalyze transglycosylation using ''p''NP-α-L-Fuc as donor substrate <cite>Benesova2015 Lezyk2016</cite>, a retaining mechanism has been inferred.

== Catalytic Residues ==
The catalytic residues of GH151 are unknown.

== Three-dimensional structures ==
No three-dimensional structures have been solved for GH151.

== Family Firsts ==
;First stereochemistry determination: Not yet identified.
;First catalytic nucleophile identification: Not yet identified.
;First general acid/base residue identification: Not yet identified.
;First 3-D structure: Not yet solved.

== References ==
<biblio>

#Sela2012 pmid=22138995
#Benesova2015 pmid=26013545
#Lezyk2016 pmid=26800369
</biblio>

[[Category:Glycoside Hydrolase Families|GH151]]

User:David Teze

2020-01-28T18:44:39Z

2020-01-07T19:42:36Z

David Teze: GH107 mechanism

GH107 mechanism

Glycoside Hydrolase Family 107

2019-12-13T18:00:19Z

David Teze:

{{UnderConstruction}}
* [[Author]]: ^^^David Teze^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH107'''
|-
|'''Clan'''
|GH-R
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH107.html
|}
</div>


== Substrate specificities ==
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.

== Kinetics and Mechanism ==

The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].

[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]
<br style="clear: both" />

== Catalytic Residues ==
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite>

== Three-dimensional structures ==
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite>

[[Image:GH107_full.png|500px]]
[[Image:20191213_GH107-zoom.png|500px]]
<br style="clear: both" />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).

== Family Firsts ==
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite>
;First catalytic nucleophile identification: The catalytic nucleophile has been identified as a catalytic residue by two simultaneous studies, in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite>
;First general acid/base residue identification: The catalytic histidine has been identified in 2018.<cite>Vickers2018</cite>
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite>

== References ==
<biblio>
#Colin2006 pmid=16880504
#Vickers2018 pmid=30282808
#Shultz-Johansen2018 pmid=30230202
</biblio>

[[Category:Glycoside Hydrolase Families|GH107]]

Glycoside Hydrolase Family 107

2019-12-13T17:59:50Z

David Teze:

{{UnderConstruction}}
* [[Author]]: ^^^David Teze^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH107'''
|-
|'''Clan'''
|GH-R
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH107.html
|}
</div>


== Substrate specificities ==
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.

== Kinetics and Mechanism ==

The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].

[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]
<br style="clear: both" />

== Catalytic Residues ==
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite>

== Three-dimensional structures ==
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite>

[[Image:GH107_full.png|600px]]
[[Image:20191213_GH107-zoom.png|600px]]
<br style="clear: both" />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).

== Family Firsts ==
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite>
;First catalytic nucleophile identification: The catalytic nucleophile has been identified as a catalytic residue by two simultaneous studies, in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite>
;First general acid/base residue identification: The catalytic histidine has been identified in 2018.<cite>Vickers2018</cite>
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite>

== References ==
<biblio>
#Colin2006 pmid=16880504
#Vickers2018 pmid=30282808
#Shultz-Johansen2018 pmid=30230202
</biblio>

[[Category:Glycoside Hydrolase Families|GH107]]

Glycoside Hydrolase Family 107

2019-12-13T17:59:17Z

David Teze:

{{UnderConstruction}}
* [[Author]]: ^^^David Teze^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH107'''
|-
|'''Clan'''
|GH-R
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH107.html
|}
</div>


== Substrate specificities ==
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.

== Kinetics and Mechanism ==

The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].

[[Image:20191213 Gh107.png|thumb|left|600px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]
<br style="clear: both" />

== Catalytic Residues ==
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite>

== Three-dimensional structures ==
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite>

[[Image:GH107_full.png|600px]]
[[Image:20191213_GH107-zoom.png|600px]]
<br style="clear: both" />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).

== Family Firsts ==
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite>
;First catalytic nucleophile identification: The catalytic nucleophile has been identified as a catalytic residue by two simultaneous studies, in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite>
;First general acid/base residue identification: The catalytic histidine has been identified in 2018.<cite>Vickers2018</cite>
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite>

== References ==
<biblio>
#Colin2006 pmid=16880504
#Vickers2018 pmid=30282808
#Shultz-Johansen2018 pmid=30230202
</biblio>

[[Category:Glycoside Hydrolase Families|GH107]]

Glycoside Hydrolase Family 107

2019-12-13T17:51:47Z

Glycoside Hydrolase Family 107

2019-12-13T13:55:17Z

David Teze:

2019-12-13T13:24:36Z

David Teze:

{{UnderConstruction}}
* [[Author]]: ^^^David Teze^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH107'''
|-
|'''Clan'''
|GH-R
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH107.html
|}
</div>


== Substrate specificities ==
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Members of the GH107 family were first described in 2006.<cite>Colin2006</cite>

== Kinetics and Mechanism ==
The mechanism was proven to be [[retaining]] by observation of the formation of an alpha-linked mercaptoethanol by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].
[[Image:20191213_Gh107.png|thumb|left|600px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]

<br style="clear: both" />

== Catalytic Residues ==
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans'', despite its structure was maintained.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneous paper.<cite>Shultz-Johansen2018</cite>

== Three-dimensional structures ==
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite>

== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
;First catalytic nucleophile identification: The catalytic nucleophile has been identified as a catalytic residue by two simultaneous studies, in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite>
;First general acid/base residue identification: The catalytic histidine has been identified in 2018.<cite>Vickers2018</cite>
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite>

== References ==
<biblio>
#Colin2006 pmid=16880504
#Vickers2018 pmid=30282808
#Shultz-Johansen2018 pmid=30230202
#Cantarel2009 pmid=18838391

#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
</biblio>

[[Category:Glycoside Hydrolase Families|GH107]]