Glycoside Hydrolase Family 158 - Revision history

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

2021-12-18T21:15:10Z

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

Kazune Tamura at 22:28, 10 April 2020

2020-04-10T22:28:08Z

Harry Brumer: /* Family Firsts */

2020-04-10T21:55:39Z

Family Firsts

Harry Brumer: Curator approved

2020-04-10T21:53:48Z

Curator approved

Harry Brumer at 21:52, 10 April 2020

2020-04-10T21:52:56Z

Harry Brumer at 18:51, 27 March 2020

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Harry Brumer at 18:48, 27 March 2020

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Harry Brumer at 18:47, 27 March 2020

2020-03-27T18:47:59Z

Harry Brumer at 18:28, 27 March 2020

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Harry Brumer at 18:27, 27 March 2020

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 {{CuratorApproved}}
-* [[Author]]: ^^^Kazune Tamura^^^
+* [[Author]]: [[User:Kazune Tamura|Kazune Tamura]]
-* [[Responsible Curator]]:  ^^^Harry Brumer^^^
+* [[Responsible Curator]]:  [[User:Harry Brumer|Harry Brumer]]
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 <biblio>
 #Helbert2019 pmid=30850540
-#Dejean2020 Déjean G, Tamura K, Cabrera A, Jain N, Pudlo NA, Pereira G, Viborg AH, Van Petegem F, Martens EC, Brumer H. 2020. Synergy between cell-surface glycosidases and glycan-binding proteins dictates the utilization of specific beta(1,3)-glucans by human gut Bacteroides. mBio 11:e00095-20. [https://doi.org/10.1128/mBio.00095-20 DOI:10.1128/mBio.00095-20]
+#Dejean2020 pmid=32265336
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH158]]

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 ;First stereochemistry determination: Retention of product anomeric stereochemistry by BuGH158 from ''Bacteroides uniformis'' using <sup>1</sup>H NMR <cite>Dejean2020</cite>.
 ;First [[catalytic nucleophile]] identification: E220 in BuGH158 from ''Bacteroides uniformis'' by tertiary structural homology and kinetic analysis of a site-directed mutant <cite>Dejean2020</cite>.
-;First [[general acid/base]] residue identification: E137 in BuGH158 from ''Bacteroides uniformis'' by tertiary structural hmology and kinetic analysis of a site-directed mutant <cite>Dejean2020</cite>.
+;First [[general acid/base]] residue identification: E137 in BuGH158 from ''Bacteroides uniformis'' by tertiary structural homology and kinetic analysis of a site-directed mutant <cite>Dejean2020</cite>.
 ;First 3-D structure: BuGH158 from ''Bacteroides uniformis'' by X-ray crystallography <cite>Dejean2020</cite>.

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-<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
+{{CuratorApproved}}
 * [[Author]]: ^^^Kazune Tamura^^^
 * [[Responsible Curator]]:  ^^^Harry Brumer^^^

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 == Substrate specificities ==
-Members of family 158 have been shown to display activity towards β(1,3)-glucans, making it the fourth [[clan]] GH-A [[glycoside hydrolase]] family known to contain β(1,3)-glucanase activity, alongside [[GH17]], [[GH128]], and GH148. The founding member of this family, Vvad_PD1638 from ''Victivallis vadensis'', was shown to be active on carboxymethyl-curdlan in a high-throughput screen <cite>Helbert2019</cite>.
+Members of family 158 have been shown to display activity towards β(1,3)-glucans, making this the fourth [[clan]] GH-A [[glycoside hydrolase]] family known to contain β(1,3)-glucanase activity, alongside [[GH17]], [[GH128]], and [[GH148]]. The founding member of this family, Vvad_PD1638 from ''Victivallis vadensis'', was shown to be active on carboxymethyl-curdlan in a high-throughput screen <cite>Helbert2019</cite>.
-BuGH158 from the human gut bacteria ''Bacteroides uniformis'' was the first GH158 member to receive detailed characterization <cite>Dejean2020</cite>. BuGH158 is an [[endo]] β(1,3)-glucanase with high specificity towards laminarin from ''Laminaria digitata'', a β(1,3)-glucan with single β(1,6)-glucose branches. BuGH158 is unable to tolerate more extensive branching as evidenced by poor activity towards other β(1,3)-glucans with longer, more frequent branches like laminarin from ''Eisenia bicyclis'' and yeast β-glucan <cite>Dejean2020</cite>. The unbranched, linear β(1,3)-glucan curdlan was also not effectively hydrolyzed by BuGH158, due the poor solubility of this polysaccharide in water (Vvad_PD1638 described above was active on a curdlan proxy that was chemically modified to increase water-solubility <cite>Helbert2019</cite>).
+BuGH158 from the human gut bacterium ''Bacteroides uniformis'' was the first GH158 member to receive detailed characterization <cite>Dejean2020</cite>. BuGH158 is an ''[[endo]]''-β(1,3)-glucanase with high specificity towards laminarin from ''Laminaria digitata'', a β(1,3)-glucan with single β(1,6)-glucose branches. BuGH158 is unable to tolerate more extensive branching as evidenced by poor activity towards other β(1,3)-glucans with longer, more frequent branches like laminarin from ''Eisenia bicyclis'' and yeast β-glucan <cite>Dejean2020</cite>. The unbranched, linear β(1,3)-glucan curdlan was also not effectively hydrolyzed by BuGH158, due the poor solubility of this polysaccharide in water (Vvad_PD1638 described above was active on a curdlan that was chemically modified to increase water-solubility <cite>Helbert2019</cite>).
 == Kinetics and Mechanism ==
-As a family within [[clan]] GH-A, GH158 members were inferred to be [[retaining]] enzymes. Retention of anomeric stereochemistry was experimentally confirmed by <sup>1</sup>H NMR on the product of hydrolysis of 2-chloro-4-nitrophenyl laminaribioside by BuGH158 from ''Bacteroides uniformis'' <cite>Dejean2020</cite>. As such, these enzymes follow the [[classical Koshland double-displacement mechanism]], which proceeds via a covalent glycosyl-enzyme [[intermediate]].
+As a family within [[clan]] GH-A, GH158 members were inferred to be [[retaining]] enzymes. Retention of anomeric stereochemistry was experimentally confirmed by <sup>1</sup>H NMR on the product of hydrolysis of 2-chloro-4-nitrophenyl laminaribioside by BuGH158 <cite>Dejean2020</cite>. Thus, GH158 members enzymes employ the [[classical Koshland double-displacement mechanism]], which proceeds via a covalent glycosyl-enzyme [[intermediate]].
 == Catalytic Residues ==
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 == Three-dimensional structures ==
 [[File:BuGH158.png|400px|thumb|right|'''Figure 1. Structure of BuGH158.''' ([{{PDBlink}}6PAL PDB ID 6PAL]) The TIM barrel domain is shown in cyan, the Ig-like domain in slate, and the catalytic nucleophile and acid/base glutamates are shown as sticks.]]
-The X-ray crystal structure of BuGH158 from ''Bacteroides uniformis'', determined by multi-wavelength anomalous dispersion, represents the founding structural representative of this family <cite>Dejean2020</cite>. The 1.8 Å structure revealed a two-domain architecture with an N-terminal (α/β)<sub>8</sub> triose phosphate isomerase (TIM) barrel domain (which is a hallmark of [[clan]] GH-A structures) and a C-terminal eight-stranded immunoglobulin (Ig)-like domain that makes extensive contacts with the TIM barrel. A loop from the Ig-like domain extends over the TIM barrel to shape the active site cleft <cite>Dejean2020</cite>.
+The X-ray crystal structure of BuGH158 from ''Bacteroides uniformis'', determined by multi-wavelength anomalous dispersion, represents the founding structural representative of this family <cite>Dejean2020</cite>. The 1.8 Å-resolution structure revealed a two-domain architecture with an N-terminal (α/β)<sub>8</sub> triose phosphate isomerase (TIM) barrel domain (the hallmark of [[clan]] GH-A structures) and a C-terminal eight-stranded immunoglobulin (Ig)-like domain that makes extensive contacts with the TIM barrel. A loop from the Ig-like domain extends over the TIM barrel to shape the active site cleft <cite>Dejean2020</cite>.
 == Family Firsts ==
-;First stereochemistry determination: Retention of product anomeric stereochemistry by BuGH158 from ''Bacteroides uniformis'' by <sup>1</sup>H NMR <cite>Dejean2020</cite>.
+;First stereochemistry determination: Retention of product anomeric stereochemistry by BuGH158 from ''Bacteroides uniformis'' using <sup>1</sup>H NMR <cite>Dejean2020</cite>.
-;First [[catalytic nucleophile]] identification: E220 in BuGH158 from ''Bacteroides uniformis'' by structural study and kinetic analysis of site-directed mutant <cite>Dejean2020</cite>.
+;First [[catalytic nucleophile]] identification: E220 in BuGH158 from ''Bacteroides uniformis'' by tertiary structural homology and kinetic analysis of a site-directed mutant <cite>Dejean2020</cite>.
-;First [[general acid/base]] residue identification: E137 in BuGH158 from ''Bacteroides uniformis'' by structural study and kinetic analysis of site-directed mutant <cite>Dejean2020</cite>.
+;First [[general acid/base]] residue identification: E137 in BuGH158 from ''Bacteroides uniformis'' by tertiary structural hmology and kinetic analysis of a site-directed mutant <cite>Dejean2020</cite>.
 ;First 3-D structure: BuGH158 from ''Bacteroides uniformis'' by X-ray crystallography <cite>Dejean2020</cite>.