Structure And Dynamics Of The Reactive State For The Histidine Methylation Process And Catalytic Mechanism Of Setd3: Insights From Quantum Mechanics/Molecular Mechanics Investigation

The SETD3 enzyme adds a methyl group to N-epsilon 2 of His73 in beta-actin, and such methylation finetunes actin's biochemical properties and cellular function. Here, quantum mechanics/molecular mechanics molecular dynamics and free energy (potential of mean force, PMF) simulations are performed to understand structural and dynamic properties of the reactive state of the SETD3-substrate complex for the methylation process and study the catalytic mechanism of the SETD3 methyltransferase. It is demonstrated that the reactive state for methylation in which His73 adopts the N-delta 1-H pi tautomeric form is stable and His73 is well positioned at the SETD3 active site for accepting the methyl group from S-adenosyl-L-methionine (SAM). Moreover, the imidazole ring of His73 in the reactive state has a similar orientation to methylated His73 (His73Me) in the product complex. The results suggest that the imidazole ring of His73 does not undergo rotation during the methyl transfer, and this suggestion is further supported by the results of the PMF simulations for the rotation around the C beta-C-gamma bond in the reactive state as well as classical MD simulations. The free energy simulations are also performed for the methyl transfer from SAM to N-epsilon 2 of the N-delta 1-H pi tautomer of His73 in wild-type SETD3 as well as in Asn255Ala and Tyr312Phe mutants. It is shown that the free energy barrier increases by approximately 2-4 kcal mol(-1) as a result of these mutations, consistent with the experimental observations. The implication for the existence of the stable reactive state for methylation with well-positioned His73 in the SETD3-substrate complex is discussed, and the origin of the increase of the free energy barrier as a result of the mutations is proposed.