QM/MM reveals the sequence of substrate binding during OPRT action

• Published in: Computational biology and chemistry 2018-06, Vol.74, p.31-38
• Main Authors: Subrahmanyeswara Rao, N.N., Deshpande, Parag A.
• Format: Article
• Language: English
• Subjects: Metalloenzymes; Orotate; Orotate phosphoribosyltransferase; Phosphoribosyl pyrophosphate; Quantum mechanics/molecular mechanics; Substrate binding
• ISSN: 1476-9271; 1476-928X
• DOI: 10.1016/j.compbiolchem.2018.02.020

[Display omitted] •QM/MM framework applied to describe PRPP and OA binding with OPRT.•Four pathways explored for metal-PRPP-OA-OPRT complex formation.•Energetics developed for all reaction pathways.•Divalent metal ions found to be essential for PRPP complexation.•A series of experimental observations of substrate binding explained. 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.