Download MendeleyStructure and loop dynamics of a chitooligosaccharide deacetylase from the marine bacterium Vibrio campbellii (harveyi).
Pongnan, S., Robinson, R.C., Lampela, O., Juffer, A., Fukamizo, T., Suginta, W.(2025) J Biological Chem 301: 110608-110608
- PubMed: 40835009
- DOI: https://doi.org/10.1016/j.jbc.2025.110608
- Primary Citation of Related Structures:
8YFP, 8YH4, 9JEN, 9JEO, 9JT0, 9JT8 - PubMed Abstract:
A chitooligosaccharide deacetylase from Vibrio campbellii (formerly Vibrio harveyi) (VhCOD) belonging to the carbohydrate esterase family 4 catalyzes Zn 2+ -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 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, which are proposed to be involved in the catalytic reaction.
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
Organizational Affiliation:
