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

McClory, James, Timson, David J., Singh, Warispreet, Zhang, Jian and Huang, Meilan (2017) Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study. The Journal of Physical Chemistry B, 121 (49). pp. 11062-11071. ISSN 1520-6106

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Isopentenyl phosphate kinase (IPK) catalyzes the Mg2+-ATP dependent 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 salt bridge 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 found that a highly conserved Gly8 on a glycine-rich loop, together with Lys14, stabilizes the transition state.

Item Type: Article
Uncontrolled Keywords: Biocatalysis, Molecular Docking Simulation, Protein Kinases/chemistry, Quantum Theory, Thermoplasma/enzymology
Subjects: F100 Chemistry
F200 Materials Science
F900 Others in Physical Sciences
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Rachel Branson
Date Deposited: 11 May 2020 14:59
Last Modified: 31 Jul 2021 18:05

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