Glycoside Hydrolase Family 125

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• Author: ^^^Alisdair Boraston^^^
• Responsible Curator: ^^^Alisdair Boraston^^^

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Glycoside Hydrolase Family GH125
Clan	GH-L
Mechanism	inverting
Active site residues	known
CAZy DB link
https://www.cazy.org/GH125.html

Substrate specificities

The currently characterized family 125 glycoside hydrolases, which include the examples from Streptococcus pneumoniae (SpGH125) and Clostridium perfringens (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues [1].

Kinetics and Mechanism

Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-O-(α-D-mannopyranosyl)-β-D-mannopyranoside by ¹H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment [1].

Catalytic Residues

The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 [1].

Three-dimensional structures

The three dimensional structures of CpGH125 (3qt3, 3qt9, and 2nvp), SpGH125 (3qpf, 3qry, and 3qsp) are available and reveal both the (α/α)₆-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from Bacteroides ovatus (3on6, and 3p2c) and one GH125 from Bacteroides thetaiotaomicron (2pov).

Family Firsts

First stereochemistry determination

¹H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry [1].

First general base identification

CpGH125 and SpGH125 (inferred from structure) [1].

First general acid identification

CpGH125 and SpGH125 (inferred from structure) [1].

First 3-D structure

The first deposited structure was that of CpGH125 (2nvp) closely followed by the deposition of structures of the Bacteroides sp. proteins. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates [1].

References

1. Gregg KJ, Zandberg WF, Hehemann JH, Whitworth GE, Deng L, Vocadlo DJ, and Boraston AB. (2011). Analysis of a new family of widely distributed metal-independent alpha-mannosidases provides unique insight into the processing of N-linked glycans. J Biol Chem. 2011;286(17):15586-96. DOI:10.1074/jbc.M111.223172 |