2ZUY

Crystal structure of exotype rhamnogalacturonan lyase YesX

2ZUY の概要

• エントリーDOI: 10.2210/pdb2zuy/pdb
• 関連するPDBエントリー: 2ZUX
• 分子名称: YesX protein, CALCIUM ION (3 entities in total)
• 機能のキーワード: beta-propeller, lyase
• 由来する生物種: Bacillus subtilis
• 細胞内の位置: Secreted : O31527
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 69207.09

構造登録者

Ochiai, A.,Itoh, T.,Mikami, B.,Hashimoto, W.,Murata, K. (登録日: 2008-10-28, 公開日: 2009-02-03, 最終更新日: 2023-11-01)

主引用文献

Ochiai, A.,Itoh, T.,Mikami, B.,Hashimoto, W.,Murata, K.
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases
J.Biol.Chem., 284:10181-10189, 2009

PubMed Abstract: A saprophytic Bacillus subtilis secretes two types of rhamnogalacturonan (RG) lyases, endotype YesW and exotype YesX, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 YesW and YesX with a significant sequence identity (67.8%) cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction. Here we show the structural determinants for substrate recognition and the mode of action in polysaccharide lyase family 11 lyases. The crystal structures of YesW in complex with rhamnose and ligand-free YesX were determined at 1.32 and 1.65 A resolution, respectively. The YesW amino acid residues such as Asn(152), Asp(172), Asn(532), Gly(533), Thr(534), and Tyr(595) in the active cleft bind to rhamnose molecules through hydrogen bonds and van der Waals contacts. Other rhamnose molecules are accommodated at the noncatalytic domain far from the active cleft, revealing that the domain possibly functions as a novel carbohydrate-binding module. A structural comparison between YesW and YesX indicates that a specific loop in YesX for recognizing the terminal saccharide molecule sterically inhibits penetration of the polymer over the active cleft. The loop-deficient YesX mutant exhibits YesW-like endotype activity, demonstrating that molecular conversion regarding the mode of action is achieved by the addition/removal of the loop for recognizing the terminal saccharide. This is the first report on a structural insight into RG-I recognition and molecular conversion of exotype to endotype in polysaccharide lyases.

PubMed: 19193638
DOI: 10.1074/jbc.M807799200

実験手法

X-RAY DIFFRACTION (1.65 Å)