Molecular Dynamics simulations with a Molecular Mechanics force field and a quite complete exploration of the QM/MM potential energy surfaces have been performed to study the D-glutamate --> L-glutamate reaction catalyzed by Bacillus subtilis glutamate racemase. The results show that the whole process involves four successive proton transfers that occur in three different steps. The Michaelis complex is already prepared to make the first proton transfer (from Cys74 to Asp10) possible. The second step involves two proton transfers (from the alpha-carbon to Cys74, and from Cys185 to the alpha-carbon), which occurs in a concerted way, although highly asynchronic. Finally, in the third step, the nascent deprotonated Cys185 is protonated by His187. The positively charged ammonium group of the substrate plays a very important key role in the reaction. It accompanies each proton transfer in a concerted and coupled way, but moving itself in the opposite direction from Asp10 to His187. Thus, the catalytic action of Bacillus subtilis glutamate racemase is driven by its own substrate of the reaction, D-glutamate.