8XIA

X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR

8XIA の概要

• エントリーDOI: 10.2210/pdb8xia/pdb
• 分子名称: XYLOSE ISOMERASE, D-xylose, MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: isomerase(intramolecular oxidoreductase)
• 由来する生物種: Streptomyces rubiginosus
• 細胞内の位置: Cytoplasm: P24300
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 43514.24

構造登録者

Carrell, H.L.,Glusker, J.P. (登録日: 1990-10-11, 公開日: 1991-10-15, 最終更新日: 2024-02-14)

主引用文献

Carrell, H.L.,Glusker, J.P.,Burger, V.,Manfre, F.,Tritsch, D.,Biellmann, J.F.
X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.
Proc.Natl.Acad.Sci.USA, 86:4440-4444, 1989

PubMed Abstract: The structures of crystalline D-xylose isomerase (D-xylose ketol-isomerase; EC 5.3.1.5) from Streptomyces rubiginosus and of its complexes with substrate and with an active-site-directed inhibitor have been determined by x-ray diffraction techniques and refined to 1.9-A resolution. This study identifies the active site, as well as two metal-binding sites. The metal ions are important in maintaining the structure of the active-site region and one of them binds C3-O and C5-O of the substrate forming a six-membered ring. This study has revealed a very close contact between histidine and C1 of a substrate, suggesting that this is the active-site base that abstracts a proton from substrate. The mechanism-based inhibitor is a substrate analog and is turned over by the enzyme to give a product that alkylates this same histidine, reinforcing our interpretation. The changes in structure of the native enzyme, the enzyme with bound substrate, and the alkylated enzyme indicate that the mechanism involves an "open-chain" conformation of substrate and that the intermediate in the isomerization reaction is probably a cis-ene diol because the active-site histidine is correctly placed to abstract a proton from C1 or C2 of the substrate. A water molecule binds to C1O and C2O of the substrate and so may act as a proton donor or acceptor in the enolization of a ring-opened substrate.

PubMed: 2734296
DOI: 10.1073/pnas.86.12.4440

実験手法

X-RAY DIFFRACTION (1.9 Å)