Glycoside Hydrolase Family 129

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• Author: ^^^Hisashi Ashida^^^
• Responsible Curator: ^^^Shinya Fushinobu^^^

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Glycoside Hydrolase Family GH129
Clan	GH-x
Mechanism	retaining
Active site residues	Asp
CAZy DB link
https://www.cazy.org/GH129.html

Substrate specificities

This family of glycoside hydrolases was recently established for NagBb from Bifidobacterium bifidum JCM 1254, which shows slight sequence similarity with Glycoside Hydrolase Family 101 endo-α-N-acetylgalactosaminidases [1]. NagBb more rapidly act on GalNAcα1-pNP than Galβ1-3GalNAcα1-pNP; therefore its substrate specificity is quite different from Glycoside Hydrolase Family 101 enzymes (EC 3.2.1.97). It is also different from those of previously known exo-α-N-acetylgalactosaminidases (EC 3.2.1.49) in Glycoside Hydrolase Family 27, Glycoside Hydrolase Family 36 and Glycoside Hydrolase Family 109. Thus, NagBb should be called as exo/endo-α-N-acetylgalactosaminidase. NagBb most preferably hydrolyzes GalNAcα1-Ser, a minimal structure of Tn antigen on mucin-type glycoproteins, suggesting that NagBb might be involved in degradation of intestinal mucins. The members of GH129 are distributed in several bifidobacterial species such as B. longum subsp. longum, B. longum subsp. infants and B. breve, which are frequently found in intestines of infants.

Kinetics and Mechanism

NagBb is a retaining enzyme. The stereochemistry of hydrolysis has been monitored by normal-phase HPLC using GalNAcα1-pNP as a substrate. GH129 is distantly related with Glycoside Hydrolase Family 101 as well as Glycoside Hydrolase Family 13 α-amylases; the latter two family members are also classified as retaining enzymes.

Catalytic Residues

Asp-435 in NagBb is predicted as catalytic nucleophile by the remote homology-based fold recognition method using Glycoside Hydrolase Family 13 α-amylase 1 (TVAI) from Thermoactinomyces vulgaris R-47 (PDB code 1JI1) as a template. Asp-330 in NagBb may be "fixer", the third invariant catalytic residue conserved in Glycoside Hydrolase Family 101 and Glycoside Hydrolase Family 13 enzymes. General acid/base residue is unknown.

Family Firsts

First stereochemistry determination

NagBb from Bifidobacterium bifidum JCM 1254 by normal-phase HPLC

First catalytic nucleophile identification

First general acid/base residue identification

First 3-D structure

References

1. Kiyohara M, Nakatomi T, Kurihara S, Fushinobu S, Suzuki H, Tanaka T, Shoda SI, Kitaoka M, Katayama T, Yamamoto K, and Ashida H. (2012). α-N-acetylgalactosaminidase from infant-associated bifidobacteria belonging to novel glycoside hydrolase family 129 is implicated in alternative mucin degradation pathway. J Biol Chem. 2012;287(1):693-700. DOI:10.1074/jbc.M111.277384 |