3EMC

Crystal structure of XynB, an intracellular xylanase from Paenibacillus barcinonensis

3EMC の概要

• エントリーDOI: 10.2210/pdb3emc/pdb
• 関連するPDBエントリー: 3EMQ 3EMZ
• 分子名称: Endo-1,4-beta-xylanase, (4S)-2-METHYL-2,4-PENTANEDIOL (3 entities in total)
• 機能のキーワード: (a/b)8 barrel, glycosidase, hydrolase, xylan degradation
• 由来する生物種: Bacillus sp. BP-23
• 細胞内の位置: Cytoplasm : O69231
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38712.20

構造登録者

Sanz-Aparicio, J.,Isorna, P.,Gonzalez, B. (登録日: 2008-09-24, 公開日: 2009-09-29, 最終更新日: 2023-11-01)

主引用文献

Gallardo, O.,Pastor, F.I.,Polaina, J.,Diaz, P.,Lysek, R.,Vogel, P.,Isorna, P.,Gonzalez, B.,Sanz-Aparicio, J.
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.
J.Biol.Chem., 285:2721-2733, 2010

PubMed Abstract: Paenibacillus barcinonensis is a soil bacterium bearing a complex set of enzymes for xylan degradation, including several secreted enzymes and Xyn10B, one of the few intracellular xylanases reported to date. The crystal structure of Xyn10B has been determined by x-ray analysis. The enzyme folds into the typical (beta/alpha)(8) barrel of family 10 glycosyl hydrolases (GH10), with additional secondary structure elements within the beta/alpha motifs. One of these loops -L7- located at the beta7 C terminus, was essential for xylanase activity as its partial deletion yielded an inactive enzyme. The loop contains residues His(249)-Glu(250), which shape a pocket opened to solvent in close proximity to the +2 subsite, which has not been described in other GH10 enzymes. This wide cavity at the +2 subsite, where methyl-2,4-pentanediol from the crystallization medium was found, is a noteworthy feature of Xyn10B, as compared with the narrow crevice described for other GH10 xylanases. Docking analysis showed that this open cavity can accommodate glucuronic acid decorations of xylo-oligosaccharides. Co-crystallization experiments with conduramine derivative inhibitors supported the importance of this open cavity at the +2 subsite for Xyn10B activity. Several mutant derivatives of Xyn10B with improved thermal stability were obtained by forced evolution. Among them, mutant xylanases S15L and M93V showed increased half-life, whereas the double mutant S15L/M93V exhibited a further increase in stability, showing a 20-fold higher heat resistance than the wild type xylanase. All the mutations obtained were located on the surface of Xyn10B. Replacement of a Ser by a Leu residue in mutant xylanase S15L can increase hydrophobic packing efficiency and fill a superficial indentation of the protein, giving rise to a more compact structure of the enzyme.

PubMed: 19940147
DOI: 10.1074/jbc.M109.064394

実験手法

X-RAY DIFFRACTION (2.1 Å)