2ITM

Crystal structure of the E. coli xylulose kinase complexed with xylulose

2ITM の概要

• エントリーDOI: 10.2210/pdb2itm/pdb
• 分子名称: Xylulose kinase, D-XYLULOSE, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: xylulokinase, xylulose, kinase, atpase, fggy kinase, transferase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 106046.88

構造登録者

di Luccio, E.,Voegtli, J.,Wilson, D.K. (登録日: 2006-10-19, 公開日: 2006-11-14, 最終更新日: 2024-02-21)

主引用文献

Di Luccio, E.,Petschacher, B.,Voegtli, J.,Chou, H.T.,Stahlberg, H.,Nidetzky, B.,Wilson, D.K.
Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli.
J.Mol.Biol., 365:783-798, 2007

PubMed Abstract: The primary metabolic route for D-xylose, the second most abundant sugar in nature, is via the pentose phosphate pathway after a two-step or three-step conversion to xylulose-5-phosphate. Xylulose kinase (XK; EC 2.7.1.17) phosphorylates D-xylulose, the last step in this conversion. The apo and D-xylulose-bound crystal structures of Escherichia coli XK have been determined and show a dimer composed of two domains separated by an open cleft. XK dimerization was observed directly by a cryo-EM reconstruction at 36 A resolution. Kinetic studies reveal that XK has a weak substrate-independent MgATP-hydrolyzing activity, and phosphorylates several sugars and polyols with low catalytic efficiency. Binding of pentulose and MgATP to form the reactive ternary complex is strongly synergistic. Although the steady-state kinetic mechanism of XK is formally random, a path is preferred in which D-xylulose binds before MgATP. Modelling of MgATP binding to XK and the accompanying conformational change suggests that sugar binding is accompanied by a dramatic hinge-bending movement that enhances interactions with MgATP, explaining the observed synergism. A catalytic mechanism is proposed and supported by relevant site-directed mutants.

PubMed: 17123542
DOI: 10.1016/j.jmb.2006.10.068

実験手法

X-RAY DIFFRACTION (2.1 Å)