Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116

Abstract

Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β-N-acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA-1116. Crystal structures of wild-type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N-terminal carbohydrate-binding domain linked to a small α+β domain and a C-terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).

Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.

“…For example, soil bacteria Silvibacterium bohemicum S15 T (Lladó et al, 2016) and "Acidisarcina polymorpha" SBC82 (Belova et al, 2018) have been reported to degrade starch, cellulose, chitin, xylan, and pectin. Genes encoding carbohydrate hydrolases indicated that strain M133 T and A. pedis KCTC 12899 T can degrade chitin (mainly from the cell wall of fungi and the exoskeleton of arthropods) using N-acetylglucosaminidase (GH20, Meekrathok et al, 2021), but not pectin (mainly from plants) using polygalacturonases (GH28) and α-rhamnosidases (CBM67, GH106).…”