Catalytic Mechanism of Diaminopimelate Epimerase: A QM/MM Investigation

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 α-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.