Glycoside Hydrolase Family 193

2026-03-07T13:41:08Z

Masahiro Nakajima:

{{UnderConstruction}}
* [[Author]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
* [[Responsible Curator]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH193'''
|-
|'''Clan'''
|GH-S
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH193.html
|}
</div>


== Substrate specificities ==
SkSGL(Sked_30460, KEGG) from Sanguibacter kedieii 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 ==
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 Talaromyces funiculosus (TfSGL), an anomer-[[inverting]] enzyme.

== 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>. 
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 Chitinophaga pinensis and Xanthomonas campestris pv. campestris) [[GH192]] (from P. gaetbulicola and Endozoicomonas elysicola), and [[GH194]] (from P. gaetbulicala) <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 X. campestris pv. campestris 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 ==
No 3D structure is determined experimentally. However, the predicted structure of SkSGL is composed of a single (α/α)6-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. 
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.

== Family Firsts ==
;First stereochemistry determination: A bacterial β-1,2-glucanase from S. kedieii by monitoring the change in optical rotation <cite>#Nakajima2025</cite>.
;First catalytic nucleophile identification: not known.
;First general acid/base residue identification: not known.
;First 3-D structure: not determined.

== References ==
<biblio>
#Nakajima2025 pmid=40411428
#Tanaka2019 pmid=30926603
#Tanaka2024 pmid=38300345
#Abe2017 pmid=28270506
</biblio>


[[Category:Glycoside Hydrolase Families|GH193]]

Glycoside Hydrolase Family 192

2026-03-07T13:40:22Z

Masahiro Nakajima:

{{UnderConstruction}}
* [[Author]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
* [[Responsible Curator]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH192'''
|-
|'''Clan'''
|GH-S
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH192.html
|}
</div>


== Substrate specificities ==
PgSGL1(H744_1c0224, KEGG) and PgSGL2(H744_2c1936, KEGG) from Photobacterium gaetbulicola and EeSGL1(A0A081KBI6, Uniprot) from Endozoicomonas elysicola were characterized as reported in 2025 <cite>Nakajima2025</cite>. The three enzymes specifically hydrolyze β-1,2-glucan to produce β-1,2-glucooligosaccharides in an endolytic manner <cite>Nakajima2025</cite>.

== 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 Talaromyces funiculosus (TfSGL), an anomer-[[inverting]] enzyme <cite>Tanaka2019</cite>.

== Catalytic Residues ==
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>). 
Similarly, D149(EeSGL1) is a residue conserved spatially with several β-1,2-glucanases; [[GH144]] (from Chitinophaga pinensis and Xanthomonas campestris pv. campestris) [[GH193]] (from Sanguibacter keddieii), and [[GH194]] (from P. gaetbulicala) <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 EeSGL1 can be obtained by superimposed with the complex structure of [[GH144]] β-1,2-glucanase from X. campestris pv. campestris 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 ==
[[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)6-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. 
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 ==
;First stereochemisty determination: A bacterial β-1,2-glucanase from P. gaetbulicola 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 E. elysicola using molecular replacement <cite>#Nakajima2025</cite>.

== References ==
<biblio>
#Nakajima2025 pmid=40411428
#Tanaka2019 pmid=30926603
#Tanaka2024 pmid=38300345
#Abe2017 pmid=28270506
</biblio>


[[Category:Glycoside Hydrolase Families|GH192]]

2026-02-26T13:29:40Z

Masahiro Nakajima:

Glycoside Hydrolase Family 192

2026-02-26T13:08:53Z

Masahiro Nakajima:

{{UnderConstruction}}
* [[Author]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
* [[Responsible Curator]]: [[User:Masahiro Nakajima|Masahiro Nakajima]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH192'''
|-
|'''Clan'''
|GH-S
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH192.html
|}
</div>


== Substrate specificities ==
PgSGL1(H744_1c0224, KEGG) and PgSGL2(H744_2c1936, KEGG) from Photobacterium gaetbulicola and EeSGL1(A0A081KBI6, Uniprot) from Endozoicomonas elysicola were characterized as reported in 2025 <cite>Nakajima2025</cite>. The three enzymes specifically hydrolyze β-1,2-glucan to produce β-1,2-glucooligosaccharides in an endolytic manner <cite>Nakajima2025</cite>.

== 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 Talaromyces funiculosus (TfSGL), an anomer-inverting enzyme <cite>Tanaka2019</cite>.

== Catalytic Residues ==
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>). 
Similarly, D149(EeSGL1) is a residue conserved spatially with several β-1,2-glucanases; [[GH144]] (from Chitinophaga pinensis and Xanthomonas campestris pv. campestris) [[GH193]] (from Sanguibacter keddieii), and [[GH194]] (from P. gaetbulicala) <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 X. campestris pv. campestris 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 ==
A ligand-free structure of EeSGL1 is available (PDB ID, 8XUJ) <cite>Nakajima2025</cite>. EeSGL1 is composed of a single (α/α)6-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.

== Family Firsts ==
;First stereochemisty determination: A bacterial β-1,2-glucanase from P. gaetbulicola 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 E. elysicola using molecular replacement <cite>#Nakajima2025</cite>.

== References ==
<biblio>
#Nakajima2025 pmid=40411428
#Tanaka2019 pmid=30926603
#Tanaka2024 pmid=38300345
#Abe2017 pmid=28270506
</biblio>


[[Category:Glycoside Hydrolase Families|GH192]]

2026-02-25T17:29:39Z

Masahiro Nakajima: