Glycoside Hydrolase Family 194 - Revision history

Masahiro Nakajima at 05:48, 14 March 2026

2026-03-14T05:48:22Z

Masahiro Nakajima at 05:34, 14 March 2026

2026-03-14T05:34:32Z

Masahiro Nakajima at 05:30, 14 March 2026

2026-03-14T05:30:15Z

Masahiro Nakajima at 04:47, 14 March 2026

2026-03-14T04:47:55Z

Masahiro Nakajima at 12:43, 7 March 2026

2026-03-07T12:43:13Z

Masahiro Nakajima at 10:33, 5 March 2026

2026-03-05T10:33:44Z

Masahiro Nakajima at 10:28, 5 March 2026

2026-03-05T10:28:51Z

Masahiro Nakajima at 10:10, 5 March 2026

2026-03-05T10:10:14Z

Masahiro Nakajima at 10:09, 5 March 2026

2026-03-05T10:09:39Z

Masahiro Nakajima at 14:01, 26 February 2026

2026-02-26T14:01:49Z

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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:GH194_pedia.png|thumb|300px|'''Fig. 1. Superimposition of PgSGL3([[GH194]]) and XcSGL([[GH144]])''' PgSGL3(PDB ID, [{{PDBlink}}8XUK 8XUK]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in light 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 PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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.
+[[Image:GH194_pedia.png|thumb|300px|'''Fig. 1. Superimposition of PgSGL3([[GH194]]) and XcSGL([[GH144]])''' PgSGL3(PDB ID, [{{PDBlink}}8XUK 8XUK]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in light 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 PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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 43: / Line 43: @@
 == Three-dimensional structures ==
-A ligand-free structure of PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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.
+[[Image:GH194_pedia.png|thumb|300px|'''Fig. 1. Superimposition of PgSGL3([[GH194]]) and XcSGL([[GH144]])''' PgSGL3(PDB ID, [{{PDBlink}}8XUK 8XUK]) and XcSGL(PDB ID, [{{PDBlink}}8XUL 8XUL]) are shown in light 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 PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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 43: / Line 43: @@
 == Three-dimensional structures ==
-A ligand-free structure of PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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.
+A ligand-free structure of PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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 ==

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 == Kinetics and Mechanism ==
-Hydrolysis of β-1,2-glucan by PgSGL3 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 PgSGL3 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 43: / Line 43: @@
 == Three-dimensional structures ==
-A ligand-free structure of PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] families. The three conserved residues are considered as residues defining the SGL clan. Among the three residues, the glutamate is the candidate general acid described above.
+A ligand-free structure of PgSGL3 is available (PDB ID, [{{PDBlink}} 8XUK]) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] 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 43: / Line 43: @@
 == Three-dimensional structures ==
-A ligand-free structure of PgSGL3 is available (PDB ID, 8XUK) <cite>#Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]].
+A ligand-free structure of PgSGL3 is available (PDB ID, 8XUK) <cite>Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]]. 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 [[GH193]] families. The three conserved residues are considered as residues defining the SGL clan.
 == Family Firsts ==
-;First stereochemistry determination: A bacterial β-1,2-glucanase from <i>P. gaetbulicola</i> by monitoring the change in optical rotation <cite>#Nakajima2025</cite>.
+;First stereochemistry determination: A bacterial β-1,2-glucanase from <i>P. gaetbulicola</i> by monitoring the change in optical rotation <cite>Nakajima2025</cite>.
 ;First general base residue identification: not known.
 ;First general acid residue identification: not known.
-;First 3-D structure: A bacterial β-1,2-glucanase from <i>P. gaetbulicola</i> using the iodide single-wavelength anomalous diffraction phasing method.
+;First 3-D structure: A bacterial β-1,2-glucanase from <i>P. gaetbulicola</i> using the iodide single-wavelength anomalous diffraction phasing method <cite>Nakajima2025</cite>.
 == References ==

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 == Substrate specificities ==
-PgSGL3(H744_1c0222, KEGG) from <i>Photobacterium gaetbulicola</i> is specific to β-1,2-glucan among polysaccharides. The enzyme hydrolyzes β-1,2-glucan endolytically to produce β-1,2-glucooligosaccharides. PgSGL3 preferentially produce β-1,2-glucooctasaccharide at the initial stage of hydrolysis of β-1,2-glucan.
+PgSGL3(H744_1c0222, KEGG) from <i>Photobacterium gaetbulicola</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. PgSGL3 preferentially produces β-1,2-glucooctasaccharide at the initial stage of hydrolysis of β-1,2-glucan.
 == Kinetics and Mechanism ==
-PgSGL3 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 PgSGL3 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 ==
-E214(PgSGL3) 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> [2]. E214Q mutant shows drastic decrease in catalytic activity compared to the wild-type enzyme [1]. E214 is also conserved across other GH-S clan families including [[GH144]], [[GH192]], and [[GH193]]. <br>Similarly, D148 (PgSGL3) 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. gaetbulicala</i>), [[GH193]] (from <i>Sanguibacter keddieii</i>) <cite>#Nakajima2025,#Abe2017</cite>. However, no complex structure with a substrate is available.
+E214(PgSGL3) is the putative general acid as this residue is structurally well-superimposed with the general acid (E262) in [[GH162]] TfSGL [2]. E214Q mutant shows drastic decrease in catalytic activity compared to the wild-type enzyme [1]. E214 is also conserved across other GH-S clan families including [[GH144]], [[GH192]], and [[GH193]]. In [[GH189]], a family related to clan GH-S, this equivalent residue acts as a catalytic acid/base <cite>Tanaka2024</cite><br>
 == Three-dimensional structures ==
-A ligand-free structure of PgSGL3 is available <cite>#Nakajima2025</cite>.
+A ligand-free structure of PgSGL3 is available (PDB ID, 8XUK) <cite>#Nakajima2025</cite>. PgSGL3 is composed of a single (α/α)<sub>6</sub>-barrel fold. The overall structure and the shape of catalytic pocket of PgSGL3 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, [[GH194]] is classified into clan GH-S, the same clan as [[GH144]].
 == Family Firsts ==
@@ Line 52: / Line 55: @@
 #Nakajima2025 pmid=40411428
 #Tanaka2019 pmid=30926603
-#Abe2017 pmid=29280506
+#Tanaka2024 pmid=38300345
 </biblio>