4LKS

Structure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens in complex with galactose

Summary for 4LKS

• Entry DOI: 10.2210/pdb4lks/pdb
• Related: 4LPL 4LQR
• Descriptor: Glycosyl hydrolase, family 31/fibronectin type III domain protein, CALCIUM ION, beta-D-galactopyranose, ... (4 entities in total)
• Functional Keywords: b-sandwich, carbohydrate-binding, galactose, sugar binding protein
• Biological source: Clostridium perfringens
• Total number of polymer chains: 2
• Total formula weight: 38428.16

Authors

Grondin, J.M.,Duan, D.,Kirlin, A.C.,Furness, H.S.,Allingham, J.S.,Smith, S.P. (deposition date: 2013-07-08, release date: 2014-12-24, Last modification date: 2023-09-20)

Primary citation

Grondin, J.M.,Duan, D.,Kirlin, A.C.,Abe, K.T.,Chitayat, S.,Spencer, H.L.,Spencer, C.,Campigotto, A.,Houliston, S.,Arrowsmith, C.H.,Allingham, J.S.,Boraston, A.B.,Smith, S.P.
Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens.
Plos One, 12:e0171606-e0171606, 2017

PubMed Abstract: Clostridium perfringens is a commensal member of the human gut microbiome and an opportunistic pathogen whose genome encodes a suite of putative large, multi-modular carbohydrate-active enzymes that appears to play a role in the interaction of the bacterium with mucin-based carbohydrates. Among the most complex of these is an enzyme that contains a presumed catalytic module belonging to glycoside hydrolase family 31 (GH31). This large enzyme, which based on its possession of a GH31 module is a predicted α-glucosidase, contains a variety of non-catalytic ancillary modules, including three CBM32 modules that to date have not been characterized. NMR-based experiments demonstrated a preference of each module for galacto-configured sugars, including the ability of all three CBM32s to recognize the common mucin monosaccharide GalNAc. X-ray crystal structures of the CpGH31 CBM32s, both in apo form and bound to GalNAc, revealed the finely-tuned molecular strategies employed by these sequentially variable CBM32s in coordinating a common ligand. The data highlight that sequence similarities to previously characterized CBMs alone are insufficient for identifying the molecular mechanism of ligand binding by individual CBMs. Furthermore, the overlapping ligand binding profiles of the three CBMs provide a fail-safe mechanism for the recognition of GalNAc among the dense eukaryotic carbohydrate networks of the colonic mucosa. These findings expand our understanding of ligand targeting by large, multi-modular carbohydrate-active enzymes, and offer unique insights into of the expanding ligand-binding preferences and binding site topologies observed in CBM32s.

PubMed: 28158290
DOI: 10.1371/journal.pone.0171606

Experimental method

X-RAY DIFFRACTION (1.5 Å)