PDBsum entry 6pv4

Hydrolase

PDB id: 6pv4

Contents

Protein chains

589 a.a.

Ligands

EDO ×23

Metals

_CA ×19

Waters ×1718

PDB id:

6pv4

Name:

Hydrolase

Title:

Structure of cpgh84a

Structure:

Glycoside hydrolase. Chain: a, b, c, d. Engineered: yes

Source:

Clostridium perfringens atcc 13124. Organism_taxid: 195103. Strain: atcc 13124 / dsm 756 / jcm 1290 / ncimb 6125 / nctc 8237 / type a. Gene: nagh, cpf_0184. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.204 R-free: 0.248

Authors:

B.Pluvinage,A.B.Boraston

Key ref:

B.Pluvinage et al. (2019). Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens. Glycobiology, 30, 49-57. PubMed id: 31701135 DOI: 10.1093/glycob/cwz069

Date:

19-Jul-19 Release date: 11-Sep-19

Protein chains

A0A0H2YRL1  (A0A0H2YRL1_CLOP1) -  Hyaluronoglucosaminidase from Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)

Seq: 1627 a.a.

Struc: 589 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.35 - hyaluronoglucosaminidase.
• Reaction: Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.

DOI no: 10.1093/glycob/cwz069

Glycobiology 30:49-57 (2019)

PubMed id: 31701135

Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens.

B.Pluvinage, P.M.Massel, K.Burak, A.B.Boraston.

ABSTRACT

The opportunistic pathogen Clostridium perfringens possesses the ability to colonize the protective mucin layer in the gastrointestinal tract. To assist this, the C. perfringens genome contains a battery of genes encoding glycoside hydrolases (GHs) that are likely active on mucin glycans, including four genes encoding family 84 GHs: CpGH84A (NagH), CpGH84B (NagI), CpGH84C (NagJ) and CpGH84D (NagK). To probe the potential advantage gained by the expansion of GH84 enzymes in C. perfringens, we undertook the structural and functional characterization of the CpGH84 catalytic modules. Here, we show that these four CpGH84 catalytic modules act as β-N-acetyl-D-glucosaminidases able to hydrolyze N- and O-glycan motifs. CpGH84A and CpGH84D displayed a substrate specificity restricted to terminal β-1,2- and β-1,6-linked N-acetyl-D-glucosamine (GlcNAc). CpGH84B and CpGH84C appear more promiscuous with activity on terminal β-1,2-, β-1,3- and β-1,6-linked GlcNAc; both possess some activity toward β-1,4-linked GlcNAc, but this is dependent upon which monosaccharide it is linked to. Furthermore, all the CpGH84s have different optimum pHs ranging from 5.2 to 7.0. Consistent with their β-N-acetyl-D-glucosaminidase activities, the structures of the four catalytic modules revealed similar folds with a catalytic site including a conserved -1 subsite that binds GlcNAc. However, nonconserved residues in the vicinity of the +1 subsite suggest different accommodation of the sugar preceding the terminal GlcNAc, resulting in subtly different substrate specificities. This structure-function comparison of the four GH84 catalytic modules from C. perfringens reveals their different biochemical properties, which may relate to how they are deployed in the bacterium's niche in the host.