New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: PH titration curves and classical molecular dynamics simulations

The mechanism of the reactions catalyzed by the pyridoxal-phosphate- independent amino acid racemases and epimerases faces the difficult task of deprotonating a relatively low acidicity proton, the amino acid's α-hydrogen, with a relatively poor base, a cysteine. In this work, we propose a mechanism for one of these enzymes, glutamate racemase (MurI), about which many controversies exist, and the roles that its active site residues may play. The titration curves and the pK1/2 values of all of the ionizable residues for different structures leading from reactants to products have been analyzed. From these results a concerted mechanism has been proposed in which the Cys70 residue would deprotonate the α-hydrogen of the substrate while, at the same time, being deprotonated by the Asp7 residue. To study the consistency of this mechanism-classical molecular dynamics (MD) simulations have been carried out along with pK1/2 calculations on the MD-generated structures. © 2007 American Chemical Society.