5B6T

Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuranosidase complexed with Pb

Summary for 5B6T

• Entry DOI: 10.2210/pdb5b6t/pdb
• Related: 5B6S
• Descriptor: Glycosyl hydrolase family 62 protein, LEAD (II) ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: coprinopsis cinerea, alpha-l-arabinofuranosidase, arabinoxylan, gh62, hemicellulose, hydrolase
• Biological source: Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (Inky cap fungus)
• Total number of polymer chains: 2
• Total formula weight: 74120.55

Authors

Tonozuka, T. (deposition date: 2016-06-01, release date: 2016-09-07, Last modification date: 2024-11-06)

Primary citation

Tonozuka, T.,Tanaka, Y.,Okuyama, S.,Miyazaki, T.,Nishikawa, A.,Yoshida, M.
Structure of the Catalytic Domain of alpha-L-Arabinofuranosidase from Coprinopsis cinerea, CcAbf62A, Provides Insights into Structure-Function Relationships in Glycoside Hydrolase Family 62
Appl. Biochem. Biotechnol., 181:511-525, 2017

PubMed Abstract: α-L-Arabinofuranosidases, belonging to the glycoside hydrolase family (GH) 62, hydrolyze the α-1,2- or α-1,3-bond to liberate L-arabinofuranose from the xylan backbone. Here, we determined the structure of the C-terminal catalytic domain of CcAbf62A, a GH62 α-L-arabinofuranosidase from Coprinopsis cinerea. CcAbf62A is composed of a five-bladed β-propeller, as observed in other GH62 enzymes. The structure near the active site of CcAbf62A is also highly homologous to those of other GH62 enzymes. However, a calcium atom in the catalytic center interacts with an asparagine residue, Asn279, which is not found in other GH62 enzymes. In addition, some residues in subsites +3R, +2NR, +3NR, and +4NR of CcAbf62A are not conserved in other GH62 enzymes. In particular, a histidine residue, His221, is uniquely observed in subsite +2NR of CcAbf62A, which is likely to influence the substrate specificity. The results obtained here suggest that the amino acid residues that interact with the xylan backbone vary among the GH62 enzymes, despite the high similarity of their overall structures.

PubMed: 27589854
DOI: 10.1007/s12010-016-2227-0

Experimental method

X-RAY DIFFRACTION (1.48 Å)