Catalytic mechanism of diaminopimelate epimerase: A QM/MM investigation

Marco Stenta, Matteo Calvaresi, Piero Altoè, Domenico Spinelli, Marco Garavelli, Roberta Galeazzi, Andrea Bottoni

Research output: Contribution to journalArticle

Abstract

A QM/MM investigation, based on a DFT(B3LYP)//Amber-ff99 potential, has been carried out to elucidate the mechanism of diaminopimelate epimerase. This enzyme catalyzes the reversible stereoconversion of one of the two stereocenters of diaminopimelate and represents a promising target for rational drug design aimed to develop new selective antibacterial therapeutic agents. The QM/MM computations show that the reaction proceeds through a highly asynchronous mechanism where the side-chain of a negatively charged Cys-73 (thiolate) deprotonates the R-carbon substrate. Simultaneously, the Cys-217 thiolic proton moves toward the same carbon atom on the opposite face, thus determining the configuration inversion. A fingerprint analysis provides a detailed description of the influence of the various residues surrounding the active site and clearly shows the electrostatic nature of the most important contributions to the catalysis.

Original languageEnglish
Pages (from-to)1915-1930
Number of pages16
JournalJournal of Chemical Theory and Computation
Volume5
Issue number7
DOIs
Publication statusPublished - Jul 14 2009

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

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  • Cite this

    Stenta, M., Calvaresi, M., Altoè, P., Spinelli, D., Garavelli, M., Galeazzi, R., & Bottoni, A. (2009). Catalytic mechanism of diaminopimelate epimerase: A QM/MM investigation. Journal of Chemical Theory and Computation, 5(7), 1915-1930. https://doi.org/10.1021/ct900004x