2D8L

Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc

2D8L の概要

• エントリーDOI: 10.2210/pdb2d8l/pdb
• 関連するBIRD辞書のPRD_ID: PRD_900058
• 分子名称: Putative glycosyl hydrolase yteR, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose (3 entities in total)
• 機能のキーワード: unsaturated rhamnogalacturonyl hydrolase, hydrolase
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 43401.02

構造登録者

Itoh, T.,Ochiai, A.,Mikami, B.,Hashimoto, W.,Murata, K. (登録日: 2005-12-06, 公開日: 2006-11-14, 最終更新日: 2024-03-13)

主引用文献

Itoh, T.,Ochiai, A.,Mikami, B.,Hashimoto, W.,Murata, K.
A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide
J.Mol.Biol., 360:573-585, 2006

PubMed Abstract: YteR, a hypothetical protein with unknown functions, is derived from Bacillus subtilis strain 168 and has an overall structure similar to that of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits little amino acid sequence identity with UGL. UGL releases unsaturated glucuronic acid from glycosaminoglycan treated with glycosaminoglycan lyases. The amino acid sequence of YteR shows a significant homology (26% identity) with the hypothetical protein YesR also from B. subtilis strain 168. To clarify the intrinsic functions of YteR and YesR, both proteins were overexpressed in Escherichia coli, purified, and characterized. Based on their gene arrangements in genome and enzyme properties, YteR and YesR were found to constitute a novel enzyme activity, "unsaturated rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and releases an unsaturated galacturonic acid. The crystal structure of YteR complexed with unsaturated chondroitin disaccharide (UGL substrate) was obtained and compared to the structure of UGL complexed with the same disaccharide. The UGL substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively. The most likely candidate catalytic residues for general acid/base are Asp143 in YteR and Asp135 in YesR. This is supported by three-dimensional structural and site-directed mutagenesis studies. These findings provide molecular insights into novel enzyme catalysis and sequential reaction mechanisms involved in RG-I depolymerization by bacteria.

PubMed: 16781735
DOI: 10.1016/j.jmb.2006.04.047

実験手法

X-RAY DIFFRACTION (1.7 Å)