4QDW

Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose

4QDW の概要

• エントリーDOI: 10.2210/pdb4qdw/pdb
• 関連するPDBエントリー: 4QDP 4QE1 4QE4 4QE5 4QEE 4QEH
• 分子名称: Xylose isomerase, NICKEL (II) ION, L-arabinose, ... (4 entities in total)
• 機能のキーワード: tim barrel, sugar isomerase, monosaccharides, isomerase
• 由来する生物種: Streptomyces rubiginosus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 43609.51

構造登録者

Kovalevsky, A.Y.,Langan, P. (登録日: 2014-05-14, 公開日: 2014-09-03, 最終更新日: 2024-02-28)

主引用文献

Langan, P.,Sangha, A.K.,Wymore, T.,Parks, J.M.,Yang, Z.K.,Hanson, B.L.,Fisher, Z.,Mason, S.A.,Blakeley, M.P.,Forsyth, V.T.,Glusker, J.P.,Carrell, H.L.,Smith, J.C.,Keen, D.A.,Graham, D.E.,Kovalevsky, A.
L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study.
Structure, 22:1287-1300, 2014

PubMed Abstract: D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that the mechanism of ring-opening is the same as for the reaction with D-xylose. Structural evidence and QM/MM calculations show that in the reactive Michaelis complex L-arabinose is distorted to the high-energy (5)S1 conformation; this may explain the apparent high KM for this sugar. MD-FEP simulations indicate that amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose were found in furanose forms when bound to XI. We propose that these complexes containing Ni(2+) cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism.

PubMed: 25132082
DOI: 10.1016/j.str.2014.07.002

実験手法

NEUTRON DIFFRACTION (1.8 Å)
X-RAY DIFFRACTION