4DVO

Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9

4DVO の概要

• エントリーDOI: 10.2210/pdb4dvo/pdb
• 関連するPDBエントリー: 4DUO
• 分子名称: Xylose isomerase, NICKEL (II) ION, sorbitol, ... (4 entities in total)
• 機能のキーワード: tim-barrel, 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: 43641.55

構造登録者

Kovalevsky, A.Y.,Hanson, L.,Langan, P. (登録日: 2012-02-23, 公開日: 2012-08-29, 最終更新日: 2024-02-28)

主引用文献

Kovalevsky, A.,Hanson, B.L.,Mason, S.A.,Forsyth, V.T.,Fisher, Z.,Mustyakimov, M.,Blakeley, M.P.,Keen, D.A.,Langan, P.
Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.
Acta Crystallogr.,Sect.D, 68:1201-1206, 2012

PubMed Abstract: D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.

PubMed: 22948921
DOI: 10.1107/S0907444912024808

実験手法

NEUTRON DIFFRACTION (2 Å)
X-RAY DIFFRACTION