Glycoside Hydrolase Family 162 - Revision history

Masahiro Nakajima at 10:17, 5 March 2026

2026-03-05T10:17:24Z

Masahiro Nakajima at 04:57, 12 July 2025

2025-07-12T04:57:09Z

Nobukiyo Tanaka at 03:03, 2 February 2024

2024-02-02T03:03:51Z

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

2021-12-18T21:17:16Z

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

Masahiro Nakajima at 06:40, 6 June 2019

2019-06-06T06:40:20Z

Harry Brumer: PDBlink

2019-06-05T15:31:26Z

PDBlink

Harry Brumer at 15:30, 5 June 2019

2019-06-05T15:30:17Z

Harry Brumer: minor text edits

2019-06-05T15:29:36Z

minor text edits

Harry Brumer: minor text edits

2019-06-05T15:21:42Z

minor text edits

Harry Brumer: Edited Fig. 2 title and legend, added PDBlink templates

2019-06-05T15:18:33Z

Edited Fig. 2 title and legend, added PDBlink templates

@@ Line 42: / Line 42: @@
 The general acid and base of ''Tf''SGL are E262 and D446, respectively <cite>Tanaka2019</cite>. Both residues are highly conserved in [[GH162]] enzymes. The general acid of ''Tf''SGL is well superimposed with an acidic residue in a [[GH144]] bacterial β-1,2-glucanase from ''Chitinophaga pinensis'' (''Cp''SGL), whereas the general base is not superimposed <cite>Tanaka2019, Abe2017</cite>. Although the reaction mechanisms of [[GH144]] enzymes are currently unclear (June 2019), structural comparison of ''Tf''SGL and [[GH144]] suggests differences in reaction mechanisms <cite>Tanaka2019</cite>.
-A structural comparison revealed that the position of the general acid residue in [[GH162]] and the candidate catalytic residue in [[GH144]] are well superimposed structurally <cite>Tanaka2024</cite>. In contrast, the positions of the other catalytic residues (or candidate catalytic residues) in [[GH162]] and [[GH144]] are completely different <cite>Tanaka2024</cite>. Furthermore, compared to clans GH-G, L, M, O, P and Q, which have the same overall structure (= (α/α)<sub>6</sub> fold) as [[GH162]] and [[GH144]], none of the positions of the catalytic residues in [[GH162]] and [[GH144]] are conserved <cite>Tanaka2024</cite>. A new clan GH-S was created for GH162 and GH144 based on these results <cite>Tanaka2024</cite>. Later, [[GH192]], [[GH193]], and [[GH194]] joined clan GH-S <cite>Nakajima2025</cite>.
+A structural comparison revealed that the position of the general acid residue in [[GH162]] and the candidate catalytic residue in [[GH144]] are well superimposed structurally <cite>Tanaka2024</cite>. In contrast, the positions of the other catalytic residues (or candidate catalytic residues) in [[GH162]] and [[GH144]] are completely different <cite>Tanaka2024</cite>. Furthermore, compared to clans GH-G, L, M, O, P and Q, which have the same overall structure (= (α/α)<sub>6</sub> fold) as [[GH162]] and [[GH144]], none of the positions of the catalytic residues in [[GH162]] and [[GH144]] are conserved <cite>Tanaka2024</cite>. A new clan GH-S was created for [[GH162]] and [[GH144]] based on these results <cite>Tanaka2024</cite>. Later, [[GH192]], [[GH193]], and [[GH194]] joined clan GH-S <cite>Nakajima2025</cite>.
 == Three-dimensional structures ==

@@ Line 42: / Line 42: @@
 The general acid and base of ''Tf''SGL are E262 and D446, respectively <cite>Tanaka2019</cite>. Both residues are highly conserved in [[GH162]] enzymes. The general acid of ''Tf''SGL is well superimposed with an acidic residue in a [[GH144]] bacterial β-1,2-glucanase from ''Chitinophaga pinensis'' (''Cp''SGL), whereas the general base is not superimposed <cite>Tanaka2019, Abe2017</cite>. Although the reaction mechanisms of [[GH144]] enzymes are currently unclear (June 2019), structural comparison of ''Tf''SGL and [[GH144]] suggests differences in reaction mechanisms <cite>Tanaka2019</cite>.
-A structural comparison revealed that the position of the general acid residue in [[GH162]] and the candidate catalytic residue in [[GH144]] are well superimposed structurally <cite>Tanaka2024</cite>. In contrast, the positions of the other catalytic residues (or candidate catalytic residues) in [[GH162]] and [[GH144]] are completely different <cite>Tanaka2024</cite>. Furthermore, compared to clans GH-G, L, M, O, P and Q, which have the same overall structure (= (α/α)<sub>6</sub> fold) as [[GH162]] and [[GH144]], none of the positions of the catalytic residues in [[GH162]] and [[GH144]] are conserved <cite>Tanaka2024</cite>. A new clan GH-S was created for GH162 and GH144 based on these results <cite>Tanaka2024</cite>.
+A structural comparison revealed that the position of the general acid residue in [[GH162]] and the candidate catalytic residue in [[GH144]] are well superimposed structurally <cite>Tanaka2024</cite>. In contrast, the positions of the other catalytic residues (or candidate catalytic residues) in [[GH162]] and [[GH144]] are completely different <cite>Tanaka2024</cite>. Furthermore, compared to clans GH-G, L, M, O, P and Q, which have the same overall structure (= (α/α)<sub>6</sub> fold) as [[GH162]] and [[GH144]], none of the positions of the catalytic residues in [[GH162]] and [[GH144]] are conserved <cite>Tanaka2024</cite>. A new clan GH-S was created for GH162 and GH144 based on these results <cite>Tanaka2024</cite>. Later, [[GH192]], [[GH193]], and [[GH194]] joined clan GH-S <cite>Nakajima2025</cite>.
 == Three-dimensional structures ==
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 #Abe2017 pmid=28270506
 #Tanaka2024 pmid=38300345
 </biblio>

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 |-
 |'''Clan'''
-|none
+|Clan-S
 |-
 |'''Mechanism'''
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 == Catalytic Residues ==
 The general acid and base of ''Tf''SGL are E262 and D446, respectively <cite>Tanaka2019</cite>. Both residues are highly conserved in [[GH162]] enzymes. The general acid of ''Tf''SGL is well superimposed with an acidic residue in a [[GH144]] bacterial β-1,2-glucanase from ''Chitinophaga pinensis'' (''Cp''SGL), whereas the general base is not superimposed <cite>Tanaka2019, Abe2017</cite>. Although the reaction mechanisms of [[GH144]] enzymes are currently unclear (June 2019), structural comparison of ''Tf''SGL and [[GH144]] suggests differences in reaction mechanisms <cite>Tanaka2019</cite>.
 == Three-dimensional structures ==
@@ Line 56: / Line 58: @@
 #Tanaka2019 pmid=30926603
 #Abe2017 pmid=28270506
 </biblio>

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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]]: ^^^Nobukiyo Tanaka^^^
+* [[Author]]: [[User:Nobukiyo Tanaka|Nobukiyo Tanaka]]
-* [[Responsible Curator]]:  ^^^Masahiro Nakajima^^^
+* [[Responsible Curator]]:  [[User:Masahiro Nakajima|Masahiro Nakajima]]
 ----

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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]]: ^^^Nobukiyo Tanaka^^^
 * [[Responsible Curator]]:  ^^^Masahiro Nakajima^^^

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 == Kinetics and Mechanism ==
 [[Image:Catalytic_mechanism_of_Tfsgl.jpeg|thumb|right|350px|'''Figure 2. Active site and reaction mechanism.''' '''(A)''' The complex of the E262Q mutant with β-1,2-glucoheptaose. The numbers beside the substrate represent the positions of subsites. The ''red'' and ''blue'' dotted lines represent the hydrogen bonds between the ligands and D177 or E262, respectively. The β-1,2-glucotriose moiety in the observed substrate is represented by a ''yellow stick''. Candidate residues for a general acid are represented by ''brown sticks''. The 262th glutamine residue is represented as a glutamic acid. '''(B)''' E262 (general acid) indirectly protonates the glycosidic bond oxygen atom via the 3-hydroxy group of the Glc moiety at subsite +2 and D446 (general base) activates the nucleophilic water via another water <cite>Tanaka2019</cite>.]]
 Hydrolysis of cyclic β-1,2-glucan by ''Tf''SGL suggests that the enzyme is ''endo''-acting <cite>Tanaka2019</cite>. The <sup>1</sup>H-NMR analysis of the anomeric configurations of hydrolysates indicates that ''Tf''SGL has an [[inverting]] mechanism. Analysis of the change of the degree of optical rotation during hydrolysis of β-1,2-glucan also supported this mechanism <cite>Tanaka2019</cite>.
@@ Line 44: / Line 43: @@
 == Three-dimensional structures ==
-[[Image:Overall_structure.jpg|thumb|350px|'''Figure 3. Overall structure of ''Tf''SGL (PDB [https://www.rcsb.org/structure/6IMU 6IMU]).''' ]]
+[[Image:Overall_structure.jpg|thumb|350px|'''Figure 3. Overall structure of ''Tf''SGL (PDB [{{PDBlink}}6IMU 6IMU]).''' ]]
 The apo-structure of the recombinant ''Tf''SGL (''Tf''SGLr) was determined at 2.0 Å using the iodide single-wavelength anomalous diffraction phasing method (PDB [{{PDBlink}}6IMU 6IMU]) <cite>Tanaka2019</cite>. The overall structure comprises an (α/α)<sub>6</sub> toroid fold <cite>Tanaka2019</cite>. The complex structures with sophorose (PDB [{{PDBlink}}6IMV 6IMV]) and the Michaelis complex of an inactive ''Tf''SGLr-mutant (E262Q) with a β-1,2-glucoheptaose (PDB [{{PDBlink}}6IMW 6IMW]) were also determined by soaking of crystals in sophorose and β-1,2-glucan, respectively <cite>Tanaka2019</cite>. ''Tf''SGLr has a cleft crossing the surface of the structure and there is a large active-site pocket at the center of the cleft <cite>Tanaka2019</cite>. Interestingly, although ''Tf''SGL and [[GH144]] enzymes are quite different in their amino acid sequences, their overall structures and the positions of the substrates in their catalytic pockets are similar <cite>Tanaka2019</cite>. ''Tf''SGLr has slight structural similarity to [[GH15]] and [[GH8]] enzymes.

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 == Substrate specificities ==
 [[Image:The_phylogenetic_tree_of_GH162_homologs.png|thumb|500px|'''Figure 1. The phylogenetic tree of GH162 homologs.''' ]]
-The defining member of [[Glycoside hydrolase]] family 162, a β-1,2-glucanase from ''Talaromyces funiculosus'' (''Tf''SGL), was identified, characterized, and structurally analyzed as reported in 2019 <cite>Tanaka2019</cite>. This enzyme specifically hydrolyzes both cyclic and linear β-1,2-glucans, which comprise a β-linked glucosyl backbone, and preferably releases sophorose (Glc-β-1,2-Glc) from the reducing end of linear β-1,2-glucan <cite>Tanaka2019</cite>. Almost all of the family members are from Eukaryotes <cite>Tanaka2019</cite>
+The defining member of [[glycoside hydrolase]] family 162, a β-1,2-glucanase from ''Talaromyces funiculosus'' (''Tf''SGL), was identified, characterized, and structurally analyzed as reported in 2019 <cite>Tanaka2019</cite>. This enzyme specifically hydrolyzes both cyclic and linear β-1,2-glucans, which comprise a β-linked glucosyl backbone, and preferably releases sophorose (Glc-β-1,2-Glc) from the reducing end of linear β-1,2-glucan <cite>Tanaka2019</cite>. Almost all of the family members are from Eukaryotes <cite>Tanaka2019</cite>
 == Kinetics and Mechanism ==

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-[[Image:The_phylogenetic_tree_of_GH162_homologs.png|thumb|500px|'''Figure 1. The phylogenetic tree of GH162 homologs.''' ]]In [[Glycoside hydrolase]] family 162, a β-1,2-glucanase only from ''Talaromyces funiculosus'' (''Tf''SGL) has been identified, characterized and structurally analyzed as of June 4th, 2019 <cite>Tanaka2019</cite>. The enzyme specifically hydrolyzes both cyclic and linear β-1,2-glucans, which comprise a β-linked glucosyl backbone, and preferably releases sophorose (Glc-β-1,2-Glc) from the reducing end of linear β-1,2-glucan <cite>Tanaka2019</cite>. Almost all of the family members are from Eukaryotes <cite>Tanaka2019</cite>
+[[Image:The_phylogenetic_tree_of_GH162_homologs.png|thumb|500px|'''Figure 1. The phylogenetic tree of GH162 homologs.''' ]]
 == Kinetics and Mechanism ==
-[[Image:Catalytic_mechanism_of_Tfsgl.jpeg|thumb|right|350px|'''Figure 2. Structurally possible pathways for a general acid (A) and the reaction mechanism (B).'''
+[[Image:Catalytic_mechanism_of_Tfsgl.jpeg|thumb|right|350px|'''Figure 2. Active site and reaction mechanism.''' '''(A)''' The complex of the E262Q mutant with β-1,2-glucoheptaose. The numbers beside the substrate represent the positions of subsites. The ''red'' and ''blue'' dotted lines represent the hydrogen bonds between the ligands and D177 or E262, respectively. The β-1,2-glucotriose moiety in the observed substrate is represented by a ''yellow stick''. Candidate residues for a general acid are represented by ''brown sticks''. The 262th glutamine residue is represented as a glutamic acid. '''(B)''' E262 (general acid) indirectly protonates the glycosidic bond oxygen atom via the 3-hydroxy group of the Glc moiety at subsite +2 and D446 (general base) activates the nucleophilic water via another water <cite>Tanaka2019</cite>.]]
-'''(A)''' The complex of the E262Q mutant with β-1,2-glucoheptaose. The numbers beside the substrate represent the positions of subsites. The ''red'' and ''blue dotted lines'' represent the hydrogen bonds between the ligands and D177 or E262, respectively. The β-1,2-glucotriose moiety in the observed substrate is represented by a ''yellow stick''. Candidate residues for a general acid are represented by ''brown sticks''. The 262th glutamine residue is represented as a glutamic acid. '''(B)''' E262 (general acid) indirectly protonates the glycosidic bond oxygen atom via the 3-hydroxy group of the Glc moiety at subsite +2 and D446 (general base) activates the nucleophilic water via another water <cite>Tanaka2019</cite>.]]Hydrolysis of cyclic β-1,2-glucan by ''Tf''SGL suggests that the enzyme is ''endo''-type <cite>Tanaka2019</cite>. The <sup>1</sup>H-NMR analysis of the anomeric configurations of hydrolysates indicates that ''Tf''SGL has an inverting mechanism. Analysis of the change of the degree of optical rotation during hydrolysis of β-1,2-glucan also supported this mechanism <cite>Tanaka2019</cite>.
 Structural analysis (see “Three-dimensional structures”) and mutational analysis suggest that D446 activates the nucleophilic water via another water as a general acid <cite>Tanaka2019</cite>. These analyses also suggest that D177 and/or E262 act as a general acid via the 3-hydroxy groups of the Glc moieties (see below) <cite>Tanaka2019</cite>. According to the action pattern analysis using β-1,2-glucopentaose derivatives deoxygenated at their 3-hydroxy groups in the first or second Glc moiety from the reducing end, E262 was clearly determined to be a general acid. The 3-hydroxy group of the Glc moiety at subsite +2 mediates protonation of glycosidic bond oxygen atom <cite>Tanaka2019</cite>. The reaction mechanism of ''Tf''SGL is quite unique in that both reaction pathways involving a general acid and a general base are non-canonical <cite>Tanaka2019</cite>.
@@ Line 41: / Line 44: @@
 == Three-dimensional structures ==
-[[Image:Overall_structure.jpg|thumb|350px|'''Figure 3. Overall structure of ''Tf''SGL (PDB [https://www.rcsb.org/structure/6IMU 6IMU]).''' ]]The apo-structure of the recombinant ''Tf''SGL (''Tf''SGLr) was determined at 2.0 Å using the iodide single-wavelength anomalous diffraction phasing method (PDB [https://www.rcsb.org/structure/6IMU 6IMU]) <cite>Tanaka2019</cite>. The overall structure comprises an (α/α)<sub>6</sub> toroid fold <cite>Tanaka2019</cite>. The complex structures with sophorose (PDB [https://www.rcsb.org/structure/6IMV 6IMV]) and the Michaelis complex of an inactive ''Tf''SGLr-mutant (E262Q) with a β-1,2-glucoheptaose (PDB [https://www.rcsb.org/structure/6IMW 6IMW]) were also determined by soaking of crystals in sophorose and β-1,2-glucan, respectively <cite>Tanaka2019</cite>. ''Tf''SGLr has a cleft crossing the surface of the structure and there is a large active pocket at the center of the cleft <cite>Tanaka2019</cite>. Interestingly, although ''Tf''SGL and [[GH144]] enzymes are quite different in their amino acid sequences, their overall structures and the positions of the substrates in their catalytic pockets are similar <cite>Tanaka2019</cite>. ''Tf''SGLr has slight structural similarity to [[GH15]] and [[GH8]] enzymes.
+[[Image:Overall_structure.jpg|thumb|350px|'''Figure 3. Overall structure of ''Tf''SGL (PDB [https://www.rcsb.org/structure/6IMU 6IMU]).''' ]]
 == Family Firsts ==
 ;First stereochemistry determination: A fungal β-1,2-glucanase from ''Talaromyces funiculosus'' by the NMR analysis and the analysis of the change of the degree of optical rotation <cite>Tanaka2019</cite>.