2GVE

Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase

2GVE の概要

• エントリーDOI: 10.2210/pdb2gve/pdb
• 関連するPDBエントリー: 1XIB 2GLK 2GUB
• 分子名称: Xylose isomerase, COBALT (II) ION (3 entities in total)
• 機能のキーワード: tim barrel-beta-alpha-barrels, two metal binding sites, protonation states of residues, isomerase
• 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: 43401.16

構造登録者

Katz, A.K.,Li, X.,Carrell, H.L.,Hanson, B.L.,Langan, P.,Coates, L.,Schoenborn, B.P.,Glusker, J.P.,Bunick, G.J. (登録日: 2006-05-02, 公開日: 2006-05-16, 最終更新日: 2023-08-30)

主引用文献

Katz, A.K.,Li, X.,Carrell, H.L.,Hanson, B.L.,Langan, P.,Coates, L.,Schoenborn, B.P.,Glusker, J.P.,Bunick, G.J.
Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.
Proc.Natl.Acad.Sci.Usa, 103:8342-8347, 2006

PubMed Abstract: Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.

PubMed: 16707576
DOI: 10.1073/pnas.0602598103

実験手法

NEUTRON DIFFRACTION (2.2 Å)