Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli

Eric Di Luccio, Barbara Petschacher, Jennifer Voegtli, Hui Ting Chou, Henning Stahlberg, Bernd Nidetzky, David K. Wilson

Research output: Contribution to journalArticle

31 Scopus citations

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 Å 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.

Original languageEnglish (US)
Pages (from-to)783-798
Number of pages16
JournalJournal of Molecular Biology
Volume365
Issue number3
DOIs
StatePublished - Jan 19 2007

Keywords

  • ATPase
  • FGGY kinase
  • mechanism
  • X-ray structure
  • xylulokinase

ASJC Scopus subject areas

  • Virology

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    Di Luccio, E., Petschacher, B., Voegtli, J., Chou, H. T., Stahlberg, H., Nidetzky, B., & Wilson, D. K. (2007). Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli. Journal of Molecular Biology, 365(3), 783-798. https://doi.org/10.1016/j.jmb.2006.10.068