Glycoside Hydrolase Family 192 - Revision history

Masahiro Nakajima at 05:46, 14 March 2026

2026-03-14T05:46:44Z

Masahiro Nakajima at 04:44, 14 March 2026

2026-03-14T04:44:44Z

Masahiro Nakajima at 13:40, 7 March 2026

2026-03-07T13:40:22Z

Masahiro Nakajima at 13:31, 7 March 2026

2026-03-07T13:31:26Z

Masahiro Nakajima at 12:48, 7 March 2026

2026-03-07T12:48:40Z

Masahiro Nakajima at 10:27, 5 March 2026

2026-03-05T10:27:46Z

Masahiro Nakajima at 13:35, 26 February 2026

2026-02-26T13:35:10Z

Masahiro Nakajima at 13:08, 26 February 2026

2026-02-26T13:08:53Z

Masahiro Nakajima at 13:02, 26 February 2026

2026-02-26T13:02:28Z

Masahiro Nakajima at 12:39, 26 February 2026

2026-02-26T12:39:33Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
 * [[Responsible Curator]]:  [[User:Masahiro Nakajima|Masahiro Nakajima]]

@@ Line 43: / Line 43: @@
 [[File:GH192 pedia.png|thumb|right|300px|'''Fig. 1. Superimposition of EeSGL1([[GH192]]) and XcSGL([[GH144]])''' EeSGL1(PDB ID, [{{PDBlink}}8XUJ 8XUJ]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in cyan and green, respectively. Residues labelled in red are the SGL-defining residues. Residues of XcSGL are labelled with Xc. This figure is modified from <cite>Nakajima2025</cite>]]
 A ligand-free structure of EeSGL1 is available (PDB ID, [{{PDBlink}}8XUJ 8XUJ]) <cite>Nakajima2025</cite>. EeSGL1 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of EeSGL1 are similar to those of [[GH144]] β-1,2-glucanases. The two candidate catalytic residues described above are well-superimposed with [[GH144]] β-1,2-glucanases. Based on the similarity, [[GH192]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH162]] represents the phylogenetically closest family to [[GH192]], even though they employ different catalytic mechanisms. <br><br>
-Clan GH-S is composed of [[GH144]], [[GH162]], [[GH192]], [[GH193]], and [[GH194]] which are distantly related families. Although [[GH189]] is also a family distantly related to these families, [[GH189]] is excluded from clan GH-S due to the difference in the reaction mechanism ([[GH189]] enzymes follow anomer-[[retaining]] mechanism). These distantly related families including [[GH189]] is called '''SGL clan''' <cite>Nakajima2025</cite>. The three residues labelled in red in the catalytic pocket (Fig 1) are conserved within [[GH144]], [[GH193]] and [[GH194]] families. The three conserved residues are considered as residues defining the SGL clan. Among the three residues, the glutamate residue is the candidate general acid described above.
+Clan GH-S is composed of [[GH144]], [[GH162]], [[GH192]], [[GH193]], and [[GH194]] which are distantly related families. Although [[GH189]] is also a family distantly related to these families, [[GH189]] is excluded from clan GH-S due to the difference in the reaction mechanism ([[GH189]] enzymes follow anomer-[[retaining]] mechanism). These distantly related families including [[GH189]] is called '''SGL clan''' <cite>Nakajima2025</cite>. The three residues labelled in red in the catalytic pocket (Fig. 1) are conserved within [[GH144]], [[GH193]] and [[GH194]] families. The three conserved residues are considered as residues defining the SGL clan. Among the three residues, the glutamate residue is the candidate general acid described above.
 == Family Firsts ==

@@ Line 41: / Line 41: @@
 == Three-dimensional structures ==
-[[File:GH192 pedia.png|thumb|right|300px|'''Fig. 1. Superimposition of EeSGL1([[GH192]]) and XcSGL([[GH144]])''' EeSGL1(PDB ID, [{{PDBlink}}8XUJ 8XUJ]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in cyan and green, respectively. Red residues are the SGL-defining residues. Residues of XcSGL are labelled with Xc. This figure is modified from <cite>Nakajima2025</cite>]]
+[[File:GH192 pedia.png|thumb|right|300px|'''Fig. 1. Superimposition of EeSGL1([[GH192]]) and XcSGL([[GH144]])''' EeSGL1(PDB ID, [{{PDBlink}}8XUJ 8XUJ]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in cyan and green, respectively. Residues labelled in red are the SGL-defining residues. Residues of XcSGL are labelled with Xc. This figure is modified from <cite>Nakajima2025</cite>]]
 A ligand-free structure of EeSGL1 is available (PDB ID, [{{PDBlink}}8XUJ 8XUJ]) <cite>Nakajima2025</cite>. EeSGL1 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of EeSGL1 are similar to those of [[GH144]] β-1,2-glucanases. The two candidate catalytic residues described above are well-superimposed with [[GH144]] β-1,2-glucanases. Based on the similarity, [[GH192]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH162]] represents the phylogenetically closest family to [[GH192]], even though they employ different catalytic mechanisms. <br><br>
 Clan GH-S is composed of [[GH144]], [[GH162]], [[GH192]], [[GH193]], and [[GH194]] which are distantly related families. Although [[GH189]] is also a family distantly related to these families, [[GH189]] is excluded from clan GH-S due to the difference in the reaction mechanism ([[GH189]] enzymes follow anomer-[[retaining]] mechanism). These distantly related families including [[GH189]] is called '''SGL clan''' <cite>Nakajima2025</cite>. The three residues labelled in red in the catalytic pocket (Fig 1) are conserved within [[GH144]], [[GH193]] and [[GH194]] families. The three conserved residues are considered as residues defining the SGL clan. Among the three residues, the glutamate residue is the candidate general acid described above.

@@ Line 41: / Line 41: @@
 == Three-dimensional structures ==
-A ligand-free structure of EeSGL1 is available (PDB ID, [{{PDBlink}} 8XUJ]) <cite>Nakajima2025</cite>. EeSGL1 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of EeSGL1 are similar to those of [[GH144]] β-1,2-glucanases. The two candidate catalytic residues described above are well-superimposed with [[GH144]] β-1,2-glucanases. Based on the similarity, [[GH192]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH162]] represents the phylogenetically closest family to [[GH192]], even though they employ different catalytic mechanisms. <br>
+[[File:GH192 pedia.png|thumb|right|300px|'''Fig. 1. Superimposition of EeSGL1([[GH192]]) and XcSGL([[GH144]])''' EeSGL1(PDB ID, [{{PDBlink}}8XUJ 8XUJ]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in cyan and green, respectively. Red residues are the SGL-defining residues. Residues of XcSGL are labelled with Xc. This figure is modified from <cite>Nakajima2025</cite>]]
 Clan GH-S is composed of [[GH144]], [[GH162]], [[GH192]], [[GH193]], and [[GH194]] which are distantly related families. Although [[GH189]] is also a family distantly related to these families, [[GH189]] is excluded from clan GH-S due to the difference in the reaction mechanism ([[GH189]] enzymes follow anomer-[[retaining]] mechanism). These distantly related families including [[GH189]] is called '''SGL clan''' <cite>Nakajima2025</cite>. The three residues labelled in red in the catalytic pocket (Fig 1) are conserved within [[GH144]], [[GH193]] and [[GH194]] families. The three conserved residues are considered as residues defining the SGL clan. Among the three residues, the glutamate residue is the candidate general acid described above.

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 == Kinetics and Mechanism ==
-Hydrolysis of β-1,2-glucan by PgSGL1 suggests that the enzyme follows anomer-inverting mechanism <cite>Nakajima2025</cite>. Analysis of the change of the degree of optical rotation during hydrolysis of β-1,2-glucan and after addition of aqueous ammonia. Sharp decrease of the degree of optical rotation by aqueous ammonia is the same pattern as in the case of [[GH162]] β-1,2-glucanase from <i>Talaromyces funiculosus</i> (TfSGL), an anomer-inverting enzyme <cite>Tanaka2019</cite>.
+Hydrolysis of β-1,2-glucan by PgSGL1 suggests that the enzyme follows anomer-[[inverting]] mechanism <cite>Nakajima2025</cite>. Analysis of the change of the degree of optical rotation during hydrolysis of β-1,2-glucan and after addition of aqueous ammonia. Sharp decrease of the degree of optical rotation by aqueous ammonia is the same pattern as in the case of [[GH162]] β-1,2-glucanase from <i>Talaromyces funiculosus</i> (TfSGL), an anomer-[[inverting]] enzyme <cite>Tanaka2019</cite>.
 == Catalytic Residues ==
@@ Line 41: / Line 41: @@
 == Three-dimensional structures ==
-A ligand-free structure of EeSGL1 is available (PDB ID, [{{PDBlink}} 8XUJ]) <cite>Nakajima2025</cite>. EeSGL1 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of EeSGL1 are similar to those of [[GH144]] β-1,2-glucanases. The two candidate catalytic residues described above are well-superimposed with [[GH144]] β-1,2-glucanases. Based on the similarity, [[GH192]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH162]] represents the phylogenetically closest family to [[GH192]], even though they employ different catalytic mechanisms.
+A ligand-free structure of EeSGL1 is available (PDB ID, [{{PDBlink}} 8XUJ]) <cite>Nakajima2025</cite>. EeSGL1 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of EeSGL1 are similar to those of [[GH144]] β-1,2-glucanases. The two candidate catalytic residues described above are well-superimposed with [[GH144]] β-1,2-glucanases. Based on the similarity, [[GH192]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH162]] represents the phylogenetically closest family to [[GH192]], even though they employ different catalytic mechanisms. <br>
 == Family Firsts ==

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 E221(EeSGL1) is the putative general acid as this residue is structurally well-superimposed with the general acid (E262) in [[GH162]] TfSGL <cite>Nakajima2025, Tanaka2019</cite>. E221Q mutant shows drastic decrease in catalytic activity compared to the wild-type enzyme <cite>Nakajima2025</cite>. E221 is also conserved across other GH-S clan families including [[GH144]], [[GH193]], and [[GH194]]. This residue is also conserved in [[GH189]], a family related to clan GH-S, as an acid/base catalyst <cite>Tanaka2024</cite>). <br>
 Similarly, D149(EeSGL1) is a residue conserved spatially with several β-1,2-glucanases; [[GH144]] (from <i>Chitinophaga pinensis</i> and <i>Xanthomonas campestris</i> pv. <i>campestris</i>) [[GH193]] (from <i>Sanguibacter keddieii</i>), and [[GH194]] (from <i>P. gaetbulicala</i>) <cite>#Nakajima2025, #Abe2017</cite>. D149N mutant also shows drastically decreased activity against the wild-type enzyme. Mutational analysis alone is insufficient to definitively identify catalytic residues because a reaction mechanism of
-[[GH192]] is atypical. A plausible substrate binding mode of EeSGL can be obtained by superimposed with the complex structure of [[GH144]] β-1,2-glucanase from <i>X. campestris</i> pv. <i>campestris</i> with β-1,2-glucoheptaose. However, no nucleophilic water is observed and no clear pathway for proton transfer from a nucleophilic water to a general base can be traced. It should be noted that the position of D149 (EeSGL1) does not correspond to that of the general base in [[GH162]] TfSGL nor to the nucleophile in [[GH189]] β-1,2-glucanotransferase <cite>Tanaka2019, Tanaka2024, Nakajima2025</cite>, which suggests a difference in reaction mechanism between these families.
+[[GH192]] is atypical. A plausible substrate binding mode of EeSGL1 can be obtained by superimposed with the complex structure of [[GH144]] β-1,2-glucanase from <i>X. campestris</i> pv. <i>campestris</i> with β-1,2-glucoheptaose. However, no nucleophilic water is observed and no clear pathway for proton transfer from a nucleophilic water to a general base can be traced. It should be noted that the position of D149 (EeSGL1) does not correspond to that of the general base in [[GH162]] TfSGL nor to the nucleophile in [[GH189]] β-1,2-glucanotransferase <cite>Tanaka2019, Tanaka2024, Nakajima2025</cite>, which suggests a difference in reaction mechanism between these families.
 == Three-dimensional structures ==