Catalytic Mechanism of Formate Dehydrogenase: Does Rotation of Formate Provide the Impetus for Surmounting the Activation Energy Barrier?

Abstract

AbstractFormate oxidation by Candida boidinii formate dehydrogenase was recently subjected to QM/MM MD simulations (Q. Guo et al., Biochemistry 55, 2016, 2760–2771). Inspection of snapshots from the reported umbrella sampling of the reactants state region provided two interesting observations. Firstly, an ester bond between formate and nicotinamide spontaneously formed and subsequently dissociated. Such an ester adduct was previously predicted to form with negligible energy barrier in gas phase but was so far not reported in QM/MM MD simulations. Secondly, two snapshots were identified as possible near‐attack conformations (NACs) from which the transition state (TS) can be reached by unhindered rotation of formate about its O─O axis. The NACs differ from each other in the direction of rotation required to attain TS. Calculation of natural orbitals for chemical valence channels indicated genesis of the new C─H bond already at the NAC stage. Both NACs feature a nonlinear C(formate)–H(formate)–C(nicotinamide) angle, approaching linearity only in the TS. We believe that due to the particular conception of the active site which profits from the unique triangular shape of the substrate, the formate ion can reach the TS more easily through this rotational movement than through parallel shift along the C─H vector, as previously assumed.