QM/MM reveals the sequence of substrate binding during OPRT action.Comput Biol Chem. 2018 Jun; 74:31-38.CB
Computational investigation of orotate phosphoribosyltransferase (OPRT) action, an enzymatic reaction between phosphoribosyl pyrophosphate (PRPP) and orotic acid (OA) to yield orotidine 5'-monophosphate (OMP), was carried out. Insights into the pathways of the substrate attack step of the reaction were developed under the quantum mechanics/molecular mechanics framework with S. cerevisiae strain as the representative enzyme bearer. Four pathways were proposed for PRPP and OA binding differing in the sequence of PRPP, OA and Mg2+ ion complexation with OPRT. The formation of Mg2+-OPRT complex was accompanied by a small energy change while the largest stabilization was observed for the formation of Mg2+-PRPP complex supporting the experimental observation of Mg2+-PRPP complex as the true substrate for the reaction. Formation of PRPP-OPRT complex was found to be energetically not probable rendering the pathway requiring Mg2+-OA complex not probable. Further, PRPP migration towards the active site was found to be energetically not favoured rendering the pathway involving Mg2+-OA complexation improbable. Migration of OA and Mg2+-PRPP complex towards the active site was found to be energetically probable with a large stabilization of the system when Mg2+-PRPP complex bound to the OA-OPRT complex. This conclusively proved the sequential binding of OA and Mg2+-PRPP complexes during OPRT action.
