3VSV

The complex structure of XylC with xylose

3VSV の概要

• エントリーDOI: 10.2210/pdb3vsv/pdb
• 関連するPDBエントリー: 3VST 3VSU
• 分子名称: Xylosidase, beta-D-xylopyranose, alpha-D-xylopyranose, ... (4 entities in total)
• 機能のキーワード: glycoside hydrolase, beta-xylosidase, product inhibition, hydrolase
• 由来する生物種: Thermoanaerobacterium
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 296636.14

構造登録者

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. (登録日: 2012-05-09, 公開日: 2013-02-27, 最終更新日: 2023-11-08)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.48 Å)