2NLX

Crystal structure of the apo E. coli xylulose kinase

Summary for 2NLX

• Entry DOI: 10.2210/pdb2nlx/pdb
• Related: 2ITM
• Descriptor: Xylulose kinase (2 entities in total)
• Functional Keywords: xylulokinase, fggy kinase, atpase, xylulose, kinase, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 105338.04

Authors

di Luccio, E.,Voegtli, J.,Wilson, D.K. (deposition date: 2006-10-20, release date: 2006-11-14, Last modification date: 2023-12-27)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.7 Å)