Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study

James McClory, David Timson, Warispreet Singh, Jian Zhang, Meilan Huang

Research output: Contribution to journalArticle

Abstract

Mg2+-ATPdependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the catalytically competent structure in complex with the metal ion Mg2+ and elucidate the phosphorylation reaction mechanism using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99). Comparing the substrate- bound and substrate-free IPK complexes, we observed that substrate binding results in significant conformational change of three residues Lys204, Glu207, and Lys211 located on the αG helix to form a strong saltbridge network with Asp145, which in turn tethers the invariant Ser142 via H-bond interaction. The conformational change shuts the subtrate entrance channel formed between the αG and αE helices. Further, we demonstrate the phosphorylation reaction occurs with a reaction barrier of 17.58 kcal/mol, which is in agreement with the previous experimental kinetic data. We foundthat a highly conserved Gly8 on a glycine-rich loop, together with Lys14, stabilizes the transition state.
Original languageEnglish
Pages (from-to)11062-11071
Number of pages10
JournalJournal of Physical Chemistry B
Volume121
Issue number49
DOIs
Publication statusPublished - 20 Nov 2017

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Phosphorylation
Phosphotransferases
Phosphates
Substrates
Metal ions
Molecular mechanics
Biofuels
Quantum theory
Glycine
Density functional theory
Molecular dynamics
Adenosine Triphosphate
Crystal structure
Kinetics
Computer simulation
Pharmaceutical Preparations

Bibliographical note

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.jpcb.7b08770. Uploaded in accordance with the publisher's self-archiving policy.

Cite this

McClory, James ; Timson, David ; Singh, Warispreet ; Zhang, Jian ; Huang, Meilan. / Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study. In: Journal of Physical Chemistry B. 2017 ; Vol. 121, No. 49. pp. 11062-11071.
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Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study. / McClory, James; Timson, David; Singh, Warispreet; Zhang, Jian; Huang, Meilan.

In: Journal of Physical Chemistry B, Vol. 121, No. 49, 20.11.2017, p. 11062-11071.

Research output: Contribution to journalArticle

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AB - Mg2+-ATPdependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the catalytically competent structure in complex with the metal ion Mg2+ and elucidate the phosphorylation reaction mechanism using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99). Comparing the substrate- bound and substrate-free IPK complexes, we observed that substrate binding results in significant conformational change of three residues Lys204, Glu207, and Lys211 located on the αG helix to form a strong saltbridge network with Asp145, which in turn tethers the invariant Ser142 via H-bond interaction. The conformational change shuts the subtrate entrance channel formed between the αG and αE helices. Further, we demonstrate the phosphorylation reaction occurs with a reaction barrier of 17.58 kcal/mol, which is in agreement with the previous experimental kinetic data. We foundthat a highly conserved Gly8 on a glycine-rich loop, together with Lys14, stabilizes the transition state.

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