Glycoside Hydrolase Family 193

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• Author: Masahiro Nakajima
• Responsible Curator: Masahiro Nakajima

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Glycoside Hydrolase Family GH193
Clan	GH-S
Mechanism	inverting
Active site residues	not known
CAZy DB link
https://www.cazy.org/GH193.html

Substrate specificities

SkSGL(Sked_30460, KEGG) from Sanguibacter kedieii was characterized as reported in 2025 [1]. 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 [1]. 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 [1, 2]. 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 [1, 3, 4].
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) [1, 3]. 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 [1, 2, 4], 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.

Family Firsts

First stereochemistry determination

A bacterial β-1,2-glucanase from S. kedieii by monitoring the change in optical rotation [1].

First catalytic nucleophile identification

not known.

First general acid/base residue identification

not known.

First 3-D structure

not determined.

References

1. Nakajima M, Tanaka N, Motouchi S, Kobayashi K, Shimizu H, Abe K, Hosoyamada N, Abara N, Morimoto N, Hiramoto N, Nakata R, Takashima A, Hosoki M, Suzuki S, Shikano K, Fujimaru T, Imagawa S, Kawadai Y, Wang Z, Kitano Y, Nihira T, Nakai H, and Taguchi H. (2025). New glycoside hydrolase families of β-1,2-glucanases. Protein Sci. 2025;34(6):e70147. DOI:10.1002/pro.70147 |
2. Tanaka N, Nakajima M, Narukawa-Nara M, Matsunaga H, Kamisuki S, Aramasa H, Takahashi Y, Sugimoto N, Abe K, Terada T, Miyanaga A, Yamashita T, Sugawara F, Kamakura T, Komba S, Nakai H, and Taguchi H. (2019). Identification, characterization, and structural analyses of a fungal endo-β-1,2-glucanase reveal a new glycoside hydrolase family. J Biol Chem. 2019;294(19):7942-7965. DOI:10.1074/jbc.RA118.007087 |
3. Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, and Taguchi H. (2017). Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family. J Biol Chem. 2017;292(18):7487-7506. DOI:10.1074/jbc.M116.762724 |
4. Tanaka N, Saito R, Kobayashi K, Nakai H, Kamo S, Kuramochi K, Taguchi H, Nakajima M, and Masaike T. (2024). Functional and structural analysis of a cyclization domain in a cyclic β-1,2-glucan synthase. Appl Microbiol Biotechnol. 2024;108(1):187. DOI:10.1007/s00253-024-13013-9 |