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-x
Mechanism	inverting
Active site residues	known
CAZy DB link
https://www.cazy.org/GH130.html

Substrate specificities

GH130 contains phosphorylases catalyzing the phosphorolysis of β1-4mannosidic linkage at the non-reducing end of substrates. 4-O-β-D-Mannosyl-D-glucose phosphorylase (EC 2.4.1.281), β-1,4-mannooligosaccharide phosphorylase(EC 2.4.1.319), and 1,4-β-mannosyl-N-acetylglucosamine phosphorylase (EC 2.4.1.320) are members of this family. A GH130 mannoside phosphorylase, unknown human gut bacterium mannoside phosphorylase (UhgbMP), discovered by functional metagenomics of the human gut microbiota, phosphorolyzes 4-O-β-D-mannosyl-N,N'-diacetylchitobiose, and exhibits higher synthetic activity to N,N'-diacetylchitobiose as an acceptor substrate than N-acetyl-D-glucosamine.[1]

Kinetics and Mechanism

GH130 phosphorylases phosphorolyze β1-4mannosidic linkage at the non-reducing end of substrates with net inversion of anomeric configuration. Senoura et al. [2] 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 reaction mechanism of GH130 enzymes has been proposed on the basis of the three-dimensional strucuture of BfMGP[3]. In contrast to known inverting glycoside phosphorylases, whose general acid catalyst directly donates a proton to glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bond to subsite -1, and a proton is tranferred to the glycosidic oxygen from 3OH group of the mannosyl residue. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and α-mannose 1-phosphate is generated.

Catalytic Residues

Ladevèze et al. [1] compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Substitution of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation comletely abolished the activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the scicile glycosidic oxigen[3]. However, this Asp appeared to be too distant from the the scicile glycosidic oxigen for a direct protonation. Thus the proton relay mechanism described above has been posturated.

Three-dimensional structures

Three-dimensinal structure of BfMGP has been first reported as a characterized enzyme[3]. The structures of BfMGP in complex with phosphate; 4-O-β-D-mannosyl-D-glucose and phosphate; mannose, glucose, and phosphate; and α-mannose 1-phosphate were determined. The structure of catalytic domain of BfMGP is a five-bladed β-propeller fold. BfMGP forms a homohexamer. 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

BfMGP[2]

First general acid residue identification

BfMGP[3]

First sequence identification

4-O-β-D-mannosyl-D-glucose phosphorylase[2]

Ruminococcus albus β-1,4-mannooligosaccharide phosphorylase[4]

Bacteroides thetaiotaomicron 4-O-β-D-Mannosyl-D-glucose phosphorylase[5]

First 3-D structure

BfMGP[3]

.

References

1. 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 |
2. KRISHTALEVICH AN (1950). [Basic physical properties of the artificial ear]. Probl Fiziol Akust. 1950;2:101-8. | Google Books | Open Library
3. 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 |
4. 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 |
5. 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 |
6. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |

7. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). DOI: 10.1042/BJ20080382