9INT

Crystal structure of the complex of the beta,kappa-carrageenase Cgbk16A from Wenyingzhuangia fucanilytica with an oligosaccharide of furcellaran

これはPDB形式変換不可エントリーです。

9INT の概要

• エントリーDOI: 10.2210/pdb9int/pdb
• 分子名称: GH16 domain-containing protein, 3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose (3 entities in total)
• 機能のキーワード: complex, carrageenase, gh16_13, glucoside hydrolase, oligotetrasaccharide, furcellaran, hydrolase
• 由来する生物種: Wenyingzhuangia fucanilytica
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38376.60

構造登録者

Chang, Y.,Chen, F. (登録日: 2024-07-08, 公開日: 2024-07-17, 最終更新日: 2024-09-25)

主引用文献

Chen, F.,Xue, C.,Chen, G.,Mei, X.,Zheng, L.,Chang, Y.
Structural Insights into the Substrate Recognition and Catalytic Mechanism of a GH16 beta kappa-Carrageenase from Wenyingzhuangia fucanilytica.
J.Agric.Food Chem., 72:20114-20121, 2024

PubMed Abstract: Understanding the substrate specificity of carrageenases has long been of interest in biotechnology applications. So far, the structural basis of the βκ-carrageenase that hydrolyzes furcellaran, a major hybrid carrageenan, remains unclear. Here, the crystal structure of Cgbk16A_Wf, as a representative of the βκ-carrageenase from GH16_13, was determined, and the structural characteristics of this subfamily were elucidated for the first time. The substrate binding mode was clarified through a structure analysis of the hexasaccharide-bound complex and molecular docking. The binding pocket involves a conserved catalytic motif and several specific residues associated with substrate recognition. Functions of residues R88, E290, and E184 were validated through site-directed mutagenesis. Comparing βκ-carrageenase with κ-carrageenase, we proposed that their different substrate specificities are partly due to the distinct conformations of subsite -1. This research offers a comprehensive understanding of the recognition mechanism of carrageenases and provides valuable theoretical support for enzyme modification and carrageenan oligosaccharide preparation.

PubMed: 39214858
DOI: 10.1021/acs.jafc.4c05531

実験手法

X-RAY DIFFRACTION (1.56 Å)