Catalytic Mechanism of Mevalonate Kinase Revisited, a QM/MM Study

James McClory, Juntang Lin, David Timson, Jian Zhang, Meilan Huang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Mevalonate Kinase (MVK) catalyses the ATP-Mg2+ mediated phosphate transfer of mevalonate to produce mevalonate 5-phosphate and is a key kinase in the mevalonate pathway in the biosynthesis of isopentenyl diphosphate, the precursor of isoprenoid-based biofuels. However, the crystal structure in complex with the native substrate mevalonate, ATP and Mg2+ has not been resolved, which has limited the understanding of its reaction mechanism and therefore its application in the production of isoprenoid-based biofuels. Here using molecular docking, molecular dynamic (MD) simulations and a hybrid QM/MM study, we revisited the location of Mg2+ resolved in the crystal structure of MVK and determined a catalytically competent MVK structure in complex with the native substrate mevalonate and ATP.

We demonstrated that significant conformational change on a flexilble loop connecting the α6 and α7 helix is induced by the substrate binding. Further, we found that Asp204 is coordinated to the Mg2+ ion. Arg241 plays a crucial role in organizing the triphosphoryl tail of ATP for in-line phosphate transfer and stabilizing the negative charge that accumulates at the β,γ-bridging oxygen of ATP upon bond cleavage. Remarkably, we revealed that the phosphorylation of mevalonate catalyzed by MVK occurs via a direct phosphorylation mechanism, instead of the conventionally postulated catalytic base mechanism. The catalytically competent complex structure of MVK as well as the mechanism of reaction will pave the way for the rational engineering of MVK to exploit its applications in the production of biofuels.
Original languageEnglish
Pages (from-to)2423-2431
JournalOrganic and Biomolecular Chemistry
Issue number9
Early online date05 Feb 2019
DOIs
Publication statusPublished - 07 Mar 2019

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mevalonate kinase
adenosine triphosphate
Mevalonic Acid
Adenosine Triphosphate
Biofuels
phosphates
phosphorylation
Phosphorylation
Terpenes
diphosphates
Substrates
Crystal structure
Phosphates
crystal structure
biosynthesis
organizing
helices
Biosynthesis
cleavage
Molecular Dynamics Simulation

Cite this

McClory, James ; Lin, Juntang ; Timson, David ; Zhang, Jian ; Huang, Meilan. / Catalytic Mechanism of Mevalonate Kinase Revisited, a QM/MM Study. In: Organic and Biomolecular Chemistry. 2019 ; No. 9. pp. 2423-2431.
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Catalytic Mechanism of Mevalonate Kinase Revisited, a QM/MM Study. / McClory, James; Lin, Juntang; Timson, David; Zhang, Jian ; Huang, Meilan.

In: Organic and Biomolecular Chemistry, No. 9, 07.03.2019, p. 2423-2431.

Research output: Contribution to journalArticle

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AB - Mevalonate Kinase (MVK) catalyses the ATP-Mg2+ mediated phosphate transfer of mevalonate to produce mevalonate 5-phosphate and is a key kinase in the mevalonate pathway in the biosynthesis of isopentenyl diphosphate, the precursor of isoprenoid-based biofuels. However, the crystal structure in complex with the native substrate mevalonate, ATP and Mg2+ has not been resolved, which has limited the understanding of its reaction mechanism and therefore its application in the production of isoprenoid-based biofuels. Here using molecular docking, molecular dynamic (MD) simulations and a hybrid QM/MM study, we revisited the location of Mg2+ resolved in the crystal structure of MVK and determined a catalytically competent MVK structure in complex with the native substrate mevalonate and ATP. We demonstrated that significant conformational change on a flexilble loop connecting the α6 and α7 helix is induced by the substrate binding. Further, we found that Asp204 is coordinated to the Mg2+ ion. Arg241 plays a crucial role in organizing the triphosphoryl tail of ATP for in-line phosphate transfer and stabilizing the negative charge that accumulates at the β,γ-bridging oxygen of ATP upon bond cleavage. Remarkably, we revealed that the phosphorylation of mevalonate catalyzed by MVK occurs via a direct phosphorylation mechanism, instead of the conventionally postulated catalytic base mechanism. The catalytically competent complex structure of MVK as well as the mechanism of reaction will pave the way for the rational engineering of MVK to exploit its applications in the production of biofuels.

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