8YH4

Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) in complex with chitosanbiose (GlcN)2

8YH4 の概要

• エントリーDOI: 10.2210/pdb8yh4/pdb
• 分子名称: NodB homology domain-containing protein, 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose, ZINC ION, ... (5 entities in total)
• 機能のキーワード: vibrio campbellii, chito oligosaccharide deacetylase, deacetylase enzyme, ce4 family member, hydrolase
• 由来する生物種: Vibrio campbellii ATCC BAA-1116
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 179875.37

構造登録者

Sirikan, P.,Tamo, F.,Robinson, R.C.,Wipa, S. (登録日: 2024-02-27, 公開日: 2025-03-05, 最終更新日: 2025-10-22)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.128 Å)