Glycoside Hydrolase Family 130

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• Author: Wataru Saburi
• Responsible Curator: Haruhide Mori

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Glycoside Hydrolase Family GH130
Clan	GH-S
Mechanism	inverting
Active site residues	known
CAZy DB link
https://www.cazy.org/GH130.html

Substrate specificities

Family GH130 contains phosphorylases and a glycoside hydrolase acting on β-mannosides. This family was created based on the identification of 4-O-β-D-mannosyl-D-glucose phosphorylase activity (EC 2.4.1.281) for the protein (BfMGP) derived from the gene BF0772 of Bacteroides fragilis [1]. This enzyme is likely involved in the degradation of β-1,4-mannobiose together with cellobiose 2-epimerase, which converts β-1,4-mannobiose to 4-O-β-D-mannosyl-D-glucose. Other activities within the family include: β-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319) [2], 1,4-β-mannosyl-N-acetylglucosamine phosphorylase (EC 2.4.1.320) [3, 4], 1,2-β-oligomannan phosphorylase [5], β-1,2-mannnobiose phosphorylase [5], and β-1,2-mannosidase [6, 7]

Kinetics and Mechanism

GH130 phosphorylases phosphorolyze β-mannosidic linkages at the non-reducing end of substrates with net inversion of anomeric configuration affording α-mannose-1-phosphate. Senoura et al. [1] demonstrated that 4-O-β-D-mannosyl-D-glucose phosphorylase from Bacteroides fragilis (BfMGP) produces α-mannose 1-phosphate and glucose from 4-O-β-D-mannosyl-D-glucose and inorganic phosphate. A unique proton relay mechanism for GH130 enzymes was proposed on the basis of the three-dimensional strucuture of BfMGP [8]. In contrast to other inverting glycoside phosphorylases, where a general acid catalyst is proposed to directly protonate the glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is transferred intramolecularly to the glycosidic oxygen from 3OH group. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and α-mannose 1-phosphate is generated. β-1,2-Mannosidase lacks some basic amino acid residues responsible for binding to inorganic phosphate in phosphorylases, but has two Glu residues acting as general base catalyst [6, 7]. These residues could activate catalytic water to facilitate nucleophilic attack to the anomeric carbon of the mannosyl residue.

Catalytic Residues

Ladevèze et al. [4] compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Mutation of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation completely abolished the catalytic activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the glycosidic oxygen [8]. However, this Asp appeared to be too distant from the the glycosidic oxygen for direct protonation, and the proton relay mechanism described above was therefore proposed. In β-1,2-mannosidase from Dyadobacter fermentans, Glu224 and Glu265 act as general base catalyst [7] to activate catalytic water.

Three-dimensional structures

Three-dimensional structures of several GH130 phosphorylases have been reported. The structure of Bacteroides fragilis BfMGP has been reported in complex with phosphate; 4-O-β-D-mannosyl-D-glucose and phosphate; mannose, glucose, and phosphate; and α-mannose 1-phosphate [8]. BfMGP forms a homohexamer, and each monomer has a five-bladed β-propeller fold. It has long α-helices at the N- and C-termini, and these structure are predicted to be responsible for the quaternary structure formation.

Family Firsts

First stereochemistry determination

Bacteroides fragilis BfMGP [1]

First general acid residue identification

Bacteroides fragilis BfMGP [8]

First 3-D structure

Bacteroides fragilis BfMGP [8]

References

1. Senoura T, Ito S, Taguchi H, Higa M, Hamada S, Matsui H, Ozawa T, Jin S, Watanabe J, Wasaki J, and Ito S. (2011). New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase. Biochem Biophys Res Commun. 2011;408(4):701-6. DOI:10.1016/j.bbrc.2011.04.095 |
2. Kawahara R, Saburi W, Odaka R, Taguchi H, Ito S, Mori H, and Matsui H. (2012). Metabolic mechanism of mannan in a ruminal bacterium, Ruminococcus albus, involving two mannoside phosphorylases and cellobiose 2-epimerase: discovery of a new carbohydrate phosphorylase, β-1,4-mannooligosaccharide phosphorylase. J Biol Chem. 2012;287(50):42389-99. DOI:10.1074/jbc.M112.390336 |
3. Nihira T, Suzuki E, Kitaoka M, Nishimoto M, Ohtsubo K, and Nakai H. (2013). Discovery of β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans. J Biol Chem. 2013;288(38):27366-27374. DOI:10.1074/jbc.M113.469080 |
4. Ladevèze S, Tarquis L, Cecchini DA, Bercovici J, André I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, and Potocki-Véronèse G. (2013). Role of glycoside phosphorylases in mannose foraging by human gut bacteria. J Biol Chem. 2013;288(45):32370-32383. DOI:10.1074/jbc.M113.483628 |
5. Chiku K, Nihira T, Suzuki E, Nishimoto M, Kitaoka M, Ohtsubo K, and Nakai H. (2014). Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514. PLoS One. 2014;9(12):e114882. DOI:10.1371/journal.pone.0114882 |
6. Cuskin F, Baslé A, Ladevèze S, Day AM, Gilbert HJ, Davies GJ, Potocki-Véronèse G, and Lowe EC. (2015). The GH130 Family of Mannoside Phosphorylases Contains Glycoside Hydrolases That Target β-1,2-Mannosidic Linkages in Candida Mannan. J Biol Chem. 2015;290(41):25023-33. DOI:10.1074/jbc.M115.681460 |
7. Nihira T, Chiku K, Suzuki E, Nishimoto M, Fushinobu S, Kitaoka M, Ohtsubo K, and Nakai H. (2015). An inverting β-1,2-mannosidase belonging to glycoside hydrolase family 130 from Dyadobacter fermentans. FEBS Lett. 2015;589(23):3604-10. DOI:10.1016/j.febslet.2015.10.008 |
8. Nakae S, Ito S, Higa M, Senoura T, Wasaki J, Hijikata A, Shionyu M, Ito S, and Shirai T. (2013). Structure of novel enzyme in mannan biodegradation process 4-O-β-D-mannosyl-D-glucose phosphorylase MGP. J Mol Biol. 2013;425(22):4468-78. DOI:10.1016/j.jmb.2013.08.002 |