6PV4

Structure of CpGH84A

Summary for 6PV4

• Entry DOI: 10.2210/pdb6pv4/pdb
• Related: 6PV5 6PWI
• Descriptor: Glycoside Hydrolase, CALCIUM ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase, hydrolase
• Biological source: Clostridium perfringens ATCC 13124
• Total number of polymer chains: 4
• Total formula weight: 298414.83

Authors

Pluvinage, B.,Boraston, A.B. (deposition date: 2019-07-19, release date: 2019-09-11, Last modification date: 2023-10-11)

Primary citation

Pluvinage, B.,Massel, P.M.,Burak, K.,Boraston, A.B.
Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens.
Glycobiology, 30:49-57, 2019

PubMed 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.

PubMed: 31701135
DOI: 10.1093/glycob/cwz069

Experimental method

X-RAY DIFFRACTION (2.2 Å)