Structure and loop dynamics of a chitooligosaccharide deacetylase from the marine bacterium Vibrio campbellii (harveyi)

A chitooligosaccharide deacetylase from Vibrio campbellii (formerly Vibrio harveyi) (VhCOD) belonging to the carbohydrate esterase family 4 catalyzes Zn²⁺-dependent deacetylation of a specific GlcNAc residue in chitooligosaccharides. It deacetylates chitobiose, (GlcNAc)₂, to produce GlcNAc-GlcN following Michaelis-Menten kinetics. We elucidated the six crystal structures of wildtype VhCOD in ligand-free and -bound states with (GlcNAc)₂ (substrate), GlcNAc-GlcN (product), (GlcN)₂ (product analog), GlcNAc-GlcN-GlcNAc (product), or GlcNAc-GlcN-(GlcNAc)₂ (product). The structures of VhCOD comprise the carbohydrate esterase family 4 catalytic domain and the two CBM12 carbohydrate-binding domains, similar to the COD homologs from Vibrio cholerae and Vibrio parahaemolyticus. The catalytic site, where a Zn²⁺ ion is coordinated with the His-His-Asp triad and three water molecules, is surrounded by six loops (L1-L6). Comparison between the ligand-free and various bound structures uncovered full catalytic cycle, including the product release in company with a large conformational change in L4. Molecular dynamics simulation based on the crystal structures provided further insights into the loop fluctuations, which are proposed to be involved in the catalytic reaction.