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 Citations (Scopus)

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

Fingerprint

Xylulose
Adenosine Triphosphate
Escherichia coli
Pentose Phosphate Pathway
Xylose
Dimerization
xylulokinase

Keywords

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

ASJC Scopus subject areas

  • Virology

Cite this

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

Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli. / Di Luccio, Eric; Petschacher, Barbara; Voegtli, Jennifer; Chou, Hui Ting; Stahlberg, Henning; Nidetzky, Bernd; Wilson, David K.

In: Journal of Molecular Biology, Vol. 365, No. 3, 19.01.2007, p. 783-798.

Research output: Contribution to journalArticle

Di Luccio, E, Petschacher, B, Voegtli, J, Chou, HT, Stahlberg, H, Nidetzky, B & Wilson, DK 2007, 'Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli', Journal of Molecular Biology, vol. 365, no. 3, pp. 783-798. https://doi.org/10.1016/j.jmb.2006.10.068
Di Luccio E, Petschacher B, Voegtli J, Chou HT, Stahlberg H, Nidetzky B et al. Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli. Journal of Molecular Biology. 2007 Jan 19;365(3):783-798. https://doi.org/10.1016/j.jmb.2006.10.068
Di Luccio, Eric ; Petschacher, Barbara ; Voegtli, Jennifer ; Chou, Hui Ting ; Stahlberg, Henning ; Nidetzky, Bernd ; Wilson, David K. / Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli. In: Journal of Molecular Biology. 2007 ; Vol. 365, No. 3. pp. 783-798.
@article{c504b7775a18450d96f47572db1e53db,
title = "Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli",
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 {\AA} 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.",
keywords = "ATPase, FGGY kinase, mechanism, X-ray structure, xylulokinase",
author = "{Di Luccio}, Eric and Barbara Petschacher and Jennifer Voegtli and Chou, {Hui Ting} and Henning Stahlberg and Bernd Nidetzky and Wilson, {David K.}",
year = "2007",
month = "1",
day = "19",
doi = "10.1016/j.jmb.2006.10.068",
language = "English (US)",
volume = "365",
pages = "783--798",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "3",

}

TY - JOUR

T1 - Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli

AU - Di Luccio, Eric

AU - Petschacher, Barbara

AU - Voegtli, Jennifer

AU - Chou, Hui Ting

AU - Stahlberg, Henning

AU - Nidetzky, Bernd

AU - Wilson, David K.

PY - 2007/1/19

Y1 - 2007/1/19

N2 - 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.

AB - 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.

KW - ATPase

KW - FGGY kinase

KW - mechanism

KW - X-ray structure

KW - xylulokinase

UR - http://www.scopus.com/inward/record.url?scp=33845799646&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33845799646&partnerID=8YFLogxK

U2 - 10.1016/j.jmb.2006.10.068

DO - 10.1016/j.jmb.2006.10.068

M3 - Article

C2 - 17123542

AN - SCOPUS:33845799646

VL - 365

SP - 783

EP - 798

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 3

ER -