Glycoside Hydrolase Family 193 - Revision history

Masahiro Nakajima at 23:49, 20 March 2026

2026-03-20T23:49:23Z

Masahiro Nakajima at 05:47, 14 March 2026

2026-03-14T05:47:08Z

Masahiro Nakajima at 05:27, 14 March 2026

2026-03-14T05:27:45Z

Masahiro Nakajima at 04:46, 14 March 2026

2026-03-14T04:46:44Z

Masahiro Nakajima at 13:46, 7 March 2026

2026-03-07T13:46:03Z

Masahiro Nakajima at 13:41, 7 March 2026

2026-03-07T13:41:08Z

Masahiro Nakajima at 13:37, 26 February 2026

2026-02-26T13:37:23Z

Masahiro Nakajima at 13:36, 26 February 2026

2026-02-26T13:36:20Z

Masahiro Nakajima at 13:29, 26 February 2026

2026-02-26T13:29:40Z

Masahiro Nakajima at 13:07, 26 February 2026

2026-02-26T13:07:30Z

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 == Catalytic Residues ==
 E246(SkSGL) is the putative general acid as this residue in the predicted structure of SkSGL is structurally well-superimposed with the general acid (E262) in [[GH162]] TfSGL <cite>Nakajima2025, Tanaka2019</cite>. E246 (SkSGL) is also conserved across other GH-S clan families including [[GH144]], [[GH192]], and [[GH194]]. In [[GH189]], a family related to clan GH-S, this equivalent residue acts as a catalytic acid/base <cite>Nakajima2025, Abe2017, Tanaka2024</cite>. <br>
-Similarly, D160(SkSGL) is one of the candidates for the general base as D160 in the predicted structure of SkSGL 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>) [[GH192]] (from <i>P. gaetbulicola</i> and <i>Endozoicomonas elysicola</i>), and [[GH194]] (from <i>P. gaetbulicala</i>) <cite>#Nakajima2025, #Abe2017</cite>. Structural comparison alone is insufficient to definitively identify catalytic residues because a reaction mechanism of [[GH193]] is atypical. A plausible substrate binding mode of SkSGL 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 D160 (SkSGL) does not correspond to that of the general base in [[GH162]] TfSGL nor to the nucleophile in [[GH189]] β-1,2-glucanotransferase <cite>Nakajima2025, Tanaka2019, Tanaka2024</cite>, which suggests a difference in reaction mechanism between these families.
+Similarly, D160(SkSGL) is one of the candidates for the general base as D160 in predicted structure of SkSGL 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>) [[GH192]] (from <i>P. gaetbulicola</i> and <i>Endozoicomonas elysicola</i>), and [[GH194]] (from <i>P. gaetbulicala</i>) <cite>#Nakajima2025, #Abe2017</cite>. Structural comparison alone is insufficient to definitively identify catalytic residues because a reaction mechanism of [[GH193]] is atypical. A plausible substrate binding mode of SkSGL 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 D160 (SkSGL) does not correspond to that of the general base in [[GH162]] TfSGL nor to the nucleophile in [[GH189]] β-1,2-glucanotransferase <cite>Nakajima2025, Tanaka2019, Tanaka2024</cite>, which suggests a difference in reaction mechanism between these families.
 == Three-dimensional structures ==
 [[Image:GH193_pedia.png|thumb|300px|'''Fig. 1. Superimposition of SkSGL([[GH193]]) and XcSGL([[GH144]])''' SkSGL(predicted structure) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in gray 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>]]
-No 3D structure is determined experimentally. However, the predicted structure of SkSGL is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of the predicted SkSGL structure 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, [[GH193]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH189]] represents the phylogenetically closest family to [[GH193]], even though they employ different catalytic mechanisms. <br><br>
+No 3D structure is determined experimentally. However, the predicted structures of most SkSGL homologs are composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of the predicted SkSGL structure 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, [[GH193]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH189]] represents the phylogenetically closest family to [[GH193]], 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]], [[GH192]] 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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 <!-- 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]]

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 == Three-dimensional structures ==
-[[Image:GH193_Fig1.png|thumb|300px|'''Fig. 1. Superimposition of SkSGL([[GH193]]) and XcSGL([[GH144]])''' SkSGL(predicted structure) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in gray 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>]]
+[[Image:GH193_pedia.png|thumb|300px|'''Fig. 1. Superimposition of SkSGL([[GH193]]) and XcSGL([[GH144]])''' SkSGL(predicted structure) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in gray 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>]]
 No 3D structure is determined experimentally. However, the predicted structure of SkSGL is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of the predicted SkSGL structure 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, [[GH193]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH189]] represents the phylogenetically closest family to [[GH193]], 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]], [[GH192]] 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 43: / Line 43: @@
 [[Image:GH193_Fig1.png|thumb|300px|'''Fig. 1. Superimposition of SkSGL([[GH193]]) and XcSGL([[GH144]])''' SkSGL(predicted structure) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in gray 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>]]
 No 3D structure is determined experimentally. However, the predicted structure of SkSGL is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of the predicted SkSGL structure 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, [[GH193]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH189]] represents the phylogenetically closest family to [[GH193]], 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]], [[GH192]] 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]], [[GH192]] 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 ==
 No 3D structure is determined experimentally. However, the predicted structure of SkSGL is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of the predicted SkSGL structure 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, [[GH193]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH189]] represents the phylogenetically closest family to [[GH193]], 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]], [[GH192]] 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 ==
-Currently not determined.
+No 3D structure is determined experimentally. However, the predicted structure of SkSGL is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of SkSGL 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, [[GH193]] is classified into clan GH-S, the same clan as [[GH144]]. Interestingly, [[GH189]] represents the phylogenetically closest family to [[GH193]], even though they employ different catalytic mechanisms.
 == Family Firsts ==

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 == Catalytic Residues ==
-E246(SkSGL) is the putative general acid as this residue is structurally well-superimposed with the general acid (E262) in [[GH162]] β-1,2-glucanase from <i>Talaromyces funiculosus</i> <cite>#Tanaka2019</cite>. <br>
+E246(SkSGL) is the putative general acid as this residue in the predicted structure of SkSGL is structurally well-superimposed with the general acid (E262) in [[GH162]] TfSGL <cite>Nakajima2025, Tanaka2019</cite>. E246 (SkSGL) is also conserved across other GH-S clan families including [[GH144]], [[GH192]], and [[GH194]]. In [[GH189]], a family related to clan GH-S, this equivalent residue acts as a catalytic acid/base <cite>Nakajima2025, Abe2017, Tanaka2024</cite>. <br>
-D160(SkSGL) is one of the candidate for the general base as this residue is a spatially conserved residue shared with several β-1,2-glucanases; [[GH144]] (from <i>Chitinophaga pinensis</i> and <i>Xanthomonas campestris</i> pv. <i>campestris</i>) [[GH192]] (from <i>P. gaetbulicola</i> and <i>Endozoicomonas elysicola</i>), and [[GH194]] (from <i>P. gaetbulicala</i>) <cite>#Nakajima2025, #Abe2017</cite>. However, no complex structure with a substrate is available.
+Similarly, D160(SkSGL) is one of the candidates for the general base as D160 in the predicted structure of SkSGL 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>) [[GH192]] (from <i>P. gaetbulicola</i> and <i>Endozoicomonas elysicola</i>), and [[GH194]] (from <i>P. gaetbulicala</i>) <cite>#Nakajima2025, #Abe2017</cite>. Structural comparison alone is insufficient to definitively identify catalytic residues because a reaction mechanism of [[GH193]] is atypical. A plausible substrate binding mode of SkSGL 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 D160 (SkSGL) does not correspond to that of the general base in [[GH162]] TfSGL nor to the nucleophile in [[GH189]] β-1,2-glucanotransferase <cite>Nakajima2025, Tanaka2019, Tanaka2024</cite>, which suggests a difference in reaction mechanism between these families.
 == Three-dimensional structures ==
@@ Line 53: / Line 53: @@
 #Nakajima2025 pmid=40411428
 #Tanaka2019 pmid=30926603
 #Abe2017 pmid=28270506
 </biblio>

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-SkSGL(Sked_30460, KEGG) from <i>Sanguibacter kedieii</i> is specific to β-1,2-glucan among polysaccharides. The enzyme hydrolyzes β-1,2-glucan endolytically to produce β-1,2-glucooligosaccharides <cite>#Nakajima2025</cite>.
+SkSGL(Sked_30460, KEGG) from <i>Sanguibacter kedieii</i> was characterized as reported in 2025 <cite>Nakajima2025</cite>. The enzyme specifically hydrolyzes β-1,2-glucan to produce β-1,2-glucooligosaccharides in an endolytic manner.
 == Kinetics and Mechanism ==
-SkSGL follows anomer-inverting mechanism, which is determined by measuring change in optical rotation during hydrolysis of β-1,2-glucan <cite>#Nakajima2025</cite>.
+Hydrolysis of β-1,2-glucan by SkSGL 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.
 == Catalytic Residues ==