Unique kinase catalytic mechanism of AceK with a single magnesium ion

PLoS One. 2013 Aug 19;8(8):e72048. doi: 10.1371/journal.pone.0072048. eCollection 2013.

Abstract

Isocitrate dehydrogenase kinase/phosphatase (AceK) is the founding member of the protein phosphorylation system in prokaryotes. Based on the novel and unique structural characteristics of AceK recently uncovered, we sought to understand its kinase reaction mechanism, along with other features involved in the phosphotransfer process. Herein we report density functional theory QM calculations of the mechanism of the phosphotransfer reaction catalysed by AceK. The transition states located by the QM calculations indicate that the phosphorylation reaction, catalysed by AceK, follows a dissociative mechanism with Asp457 serving as the catalytic base to accept the proton delivered by the substrate. Our results also revealed that AceK prefers a single Mg(2+)-containing active site in the phosphotransfer reaction. The catalytic roles of conserved residues in the active site are discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Biocatalysis
  • Catalytic Domain
  • Computer Simulation*
  • Coordination Complexes / chemistry
  • Escherichia coli / enzymology
  • Escherichia coli Proteins / chemistry*
  • Hydrogen Bonding
  • Isocitrate Dehydrogenase
  • Magnesium / chemistry*
  • Models, Chemical
  • Models, Molecular*
  • Multienzyme Complexes / chemistry*
  • Protein Binding
  • Quantum Theory
  • Thermodynamics

Substances

  • Coordination Complexes
  • Escherichia coli Proteins
  • Multienzyme Complexes
  • Adenosine Triphosphate
  • AceK protein, E coli
  • Isocitrate Dehydrogenase
  • Magnesium

Grants and funding

This work was supported by the National Natural Science Foundation of China (No. 21133003, No. 21073015, No.21131003). In addition, this work was also supported by Specialized Research Fund for the Doctoral Program of Higher Education, No 20110003120013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.