9IJC

Crystal structure of the beta,kappa-carrageenase Cgbk16A from Wenyingzhuangia fucanilytica

This is a non-PDB format compatible entry.

Summary for 9IJC

• Entry DOI: 10.2210/pdb9ijc/pdb
• Descriptor: GH16 domain-containing protein (2 entities in total)
• Functional Keywords: apo, carrageenase, gh16_13, glucoside hydrolase, hydrolase
• Biological source: Wenyingzhuangia fucanilytica
• Total number of polymer chains: 1
• Total formula weight: 37279.66

Authors

Chang, Y.,Chen, F. (deposition date: 2024-06-22, release date: 2024-07-17, Last modification date: 2024-09-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.52 Å)