9JT0

Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) complex with Chitobiose

Summary for 9JT0

• Entry DOI: 10.2210/pdb9jt0/pdb
• Descriptor: NodB homology domain-containing protein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ZINC ION, ... (5 entities in total)
• Functional Keywords: vibrio campbellii, chito oligosaccharide deacetylase, deacetylase enzyme, ce4 family member, hydrolase
• Biological source: Vibrio campbellii ATCC BAA-1116
• Total number of polymer chains: 3
• Total formula weight: 134729.81

Authors

Sirikan, P.,Tamo, F.,Robinson, R.C.,Wipa, S. (deposition date: 2024-10-01, release date: 2025-10-01, Last modification date: 2025-10-22)

Primary citation

Pongnan, S.,Robinson, R.C.,Lampela, O.,Juffer, A.,Fukamizo, T.,Suginta, W.
Structure and loop dynamics of a chitooligosaccharide deacetylase from the marine bacterium Vibrio campbellii (harveyi).
J.Biol.Chem., 301:110608-110608, 2025

PubMed Abstract: A chitooligosaccharide deacetylase from Vibrio campbellii (formerly Vibrio harveyi) (VhCOD) belonging to the carbohydrate esterase family 4 catalyzes Zn-dependent deacetylation of a specific GlcNAc residue in chitooligosaccharides. It deacetylates chitobiose, (GlcNAc), 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) (substrate), GlcNAc-GlcN (product), (GlcN) (product analog), GlcNAc-GlcN-GlcNAc (product), or GlcNAc-GlcN-(GlcNAc) (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 Zn 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.

PubMed: 40835009
DOI: 10.1016/j.jbc.2025.110608

Experimental method

X-RAY DIFFRACTION (2.4 Å)