Glycoside Hydrolase Family 107 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:19:42Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

David Teze at 19:44, 7 January 2020

2020-01-07T19:44:32Z

Harry Brumer at 18:03, 7 January 2020

2020-01-07T18:03:14Z

Harry Brumer: /* Kinetics and Mechanism */

2020-01-07T17:59:05Z

Kinetics and Mechanism

Harry Brumer at 17:58, 7 January 2020

2020-01-07T17:58:42Z

Harry Brumer: /* Kinetics and Mechanism */

2020-01-07T17:29:14Z

Kinetics and Mechanism

Harry Brumer: /* Substrate specificities */

2020-01-07T17:28:26Z

Substrate specificities

Harry Brumer: image placement

2020-01-07T17:25:32Z

image placement

Harry Brumer at 17:24, 7 January 2020

2020-01-07T17:24:10Z

Harry Brumer: /* Three-dimensional structures */

2020-01-07T17:23:43Z

Three-dimensional structures

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
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-* [[Author]]: ^^^David Teze^^^
+* [[Author]]: [[User:David Teze|David Teze]]
-* [[Responsible Curator]]:  ^^^Al Boraston^^^
+* [[Responsible Curator]]:  [[User:Al Boraston|Al Boraston]]
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 == Kinetics and Mechanism ==
-[[Image:20191213 Gh107.png|thumb|right|500px|Figure 1: Mechanism of family GH107, according to <cite>Vickers2018</cite>.]]
+[[Image:20200107Gh107.png|thumb|right|500px|Figure 1: Mechanism of family GH107, according to <cite>Vickers2018</cite>.]]
 The mechanism was demonstrated to be consistent with a [[classical Koshland double-displacement mechanism]] mechanism 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>.   The same mechanism is demonstrated by [[GH29]] members, consistent with their common membership in [[Clan]] GH-R.

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 [[Image:20191213_GH107-zoom.png|thumb|right|350px|Figure 3: ''Psychromonas sp.'' GH107 catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).]]
-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 the 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>.
+The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine (Figures 2 and 3). 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 the 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>.
+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 (Figure 2), 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 ==

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 == Kinetics and Mechanism ==
-[[Image:20191213 Gh107.png|thumb|right|500px|Figure 1: Mechanism of GH107 family, according to <cite>Vickers2018</cite>.]]
+[[Image:20191213 Gh107.png|thumb|right|500px|Figure 1: Mechanism of family GH107, according to <cite>Vickers2018</cite>.]]
 The mechanism was demonstrated to be consistent with a [[classical Koshland double-displacement mechanism]] mechanism 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>.   The same mechanism is demonstrated by [[GH29]] members, consistent with their common membership in [[Clan]] GH-R.

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 == Kinetics and Mechanism ==
-[[Image:20191213 Gh107.png|thumb|right|500px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]
+[[Image:20191213 Gh107.png|thumb|right|500px|Figure 1: Mechanism of GH107 family, according to <cite>Vickers2018</cite>.]]
 The mechanism was demonstrated to be consistent with a [[classical Koshland double-displacement mechanism]] mechanism 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>.   The same mechanism is demonstrated by [[GH29]] members, consistent with their common membership in [[Clan]] GH-R.

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 == Substrate specificities ==
-The currently characterized [[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.
+The currently characterized [[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 ==

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 == Catalytic Residues ==
 [[Image:GH107_full.png|thumb|right|350px|Figure 2: ''Psychromonas sp.'' GH107 global structure (PDB: [{{PDBlink}}6m8n 6m8n]).]]
 [[Image:20191213_GH107-zoom.png|thumb|right|350px|Figure 3: ''Psychromonas sp.'' GH107 catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).]]
 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>.