3VSU

The complex structure of XylC with xylobiose

Summary for 3VSU

• Entry DOI: 10.2210/pdb3vsu/pdb
• Related: 3VST 3VSV
• Related PRD ID: PRD_900116
• Descriptor: Xylosidase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose (3 entities in total)
• Functional Keywords: glycoside hydrolase, beta-xylosidase, product inhibition, hydrolase
• Biological source: Thermoanaerobacterium
• Total number of polymer chains: 4
• Total formula weight: 292510.57

Authors

Huang, C.H.,Sun, Y.,Ko, T.P.,Ma, Y.,Chen, C.C.,Zheng, Y.,Chan, H.C.,Pang, X.,Wiegel, J.,Shao, W.,Guo, R.T. (deposition date: 2012-05-09, release date: 2013-02-27, Last modification date: 2023-11-08)

Primary citation

Huang, C.H.,Sun, Y.,Ko, T.P.,Chen, C.C.,Zheng, Y.,Chan, H.C.,Pang, X.,Wiegel, J.,Shao, W.,Guo, R.T.
The substrate/product-binding modes of a novel GH120 beta-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485
Biochem.J., 448:401-407, 2012

PubMed Abstract: Xylan-1,4-β-xylosidase (β-xylosidase) hydrolyses xylo-oligomers at their non-reducing ends into individual xylose units. Recently, XylC, a β-xylosidase from Thermoanaerobacterium saccharolyticum JW/SL-YS485, was found to be structurally different from corresponding glycosyl hydrolases in the CAZy database (http://www.cazy.org/), and was subsequently classified as the first member of a novel family of glycoside hydrolases (GH120). In the present paper, we report three crystal structures of XylC in complex with Tris, xylobiose and xylose at 1.48-2.05 Å (1 Å=0.1 nm) resolution. XylC assembles into a tetramer, and each monomer comprises two distinct domains. The core domain is a right-handed parallel β-helix (residues 1-75 and 201-638) and the flanking region (residues 76-200) folds into a β-sandwich domain. The enzyme contains an open carbohydrate-binding cleft, allowing accommodation of longer xylo-oligosaccharides. On the basis of the crystal structures and in agreement with previous kinetic data, we propose that XylC cleaves the glycosidic bond by the retaining mechanism using two acidic residues Asp382 (nucleophile) and Glu405 (general acid/base). In addition to the active site, nine other xylose-binding sites were consistently observed in each of the four monomers, providing a possible reason for the high tolerance of product inhibition.

PubMed: 22992047
DOI: 10.1042/BJ20121359

Experimental method

X-RAY DIFFRACTION (2.05 Å)