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

A chitooligosaccharide deacetylase from Vibrio campbellii (formerly V. harveyi) ( Vh COD) belonging to the carbohydrate esterase family 4 (CE4) catalyzes Zn 2+ -dependent deacetylation of a specific N -acetylglucosamine (GlcNAc) residue in chitooligosaccharides. It deacetylates chitobiose, (GlcNAc) 2 , to produce GlcNAc-GlcN following Michaelis-Menten kinetics. We elucidated the six crystal structures of wild type Vh COD in ligand-free and bound states with (GlcNAc) 2 (substrate), GlcNAc-GlcN (product), (GlcN) 2 (product analogue), GlcNAc-GlcN-GlcNAc (product) or GlcNAc-GlcN-(GlcNAc) 2 (product). The structures of Vh COD comprise the CE4 catalytic domain and the two CBM12 carbohydrate-binding domains, similar to the COD homologues from Vibrio cholerae and Vibrio parahaemolyticus . The catalytic site, where a Zn 2+ 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, that are proposed to be involved in the catalytic reaction.