Structure-based analysis of domain function of chitin oligosaccharide deacetylase from Vibrio parahaemolyticus

•The X-ray crystal structure of Vp-COD was determined.•The Vp-COD consists of one PDD and two CBDs.•The CBDs possess ability to adhere to chitin.•The PDD can function independently as a catalytic domain.•The CBDs contribute little to stabilizing the catalytic function of PDD.

The X-ray crystal structure of chitin oligosaccharide deacetylase from Vibrio parahaemolyticus (Vp-COD) was determined at an 1.35 Å resolution. The amino acid sequence and structure of Vp-COD show that the enzyme comprises one polysaccharide deacetylase domain (PDD) and two carbohydrate-binding domains (CBDs). On the basis of a chitin-binding assay with Vp-COD and its CBDs-deleted mutant, it was confirmed that CBDs can adhere to chitin. The catalytic activity of the CBDs-deleted mutant was only mildly depressed compared with that of Vp-COD, indicating that CBDs are unlikely to affect the configuration of the active center residues in active site of PDD.