A quantum mechanics/molecular mechanics study of the catalytic mechanism and product specificity of viral histone lysine methyltransferase

There are three reaction steps in the S-adenosylmethionine (AdoMet) methylation of lysine-NH2 catalyzed by a methyltransferase. They are (i) combination of enzyme center dot Lys-NH3+ with AdoMet, (ii) substrate ionization to provide enzyme center dot AdoMet center dot Lys-NH2, and (iii) methyl transfer providing enzyme center dot AdoHcy center dot Lys-N(Me)H-2(+) and the dissociation of AdoHcy. In this study of the viral histone methyltransferase (vSET), we find that substrate ionization of vSET center dot Lys27-NH3+, vSET center dot Lys27-N(Me)H-2(+), and vSET center dot Lys27-N(Me)(2)H+ takes place upon combination with AdoMet. The presence of a water channel allows dissociation of a proton to the solvent. There is no water channel in the absence of AdoMet. That the formation of a water channel is combined with AdoMet binding was first discovered in our investigation of Rubisco large subunit methyltransferase. Via a quantum mechanics/molecular mechanics (QM/MM) approach, the calculated free energy barrier (Delta G(double dagger)) of the first methyl transfer reaction catalyzed by vSET [Lys27-NH2 + AdoMet -> Lys27-N(Me)H-2(+) + AdoHcy] equals 22.5 +/- 4.3 kcal/mol, which is in excellent agreement with the free energy barrier (21.7 kcal/mol) calculated from the experimental rate constant (0.047 min(-1)). The calculated Delta G(double dagger) of the second methyl transfer reaction [AdoMet + Lys27-N(Me)H -> AdoHcy + Lys27-N(Me)(2)H+] at the QM/MM level is 22.6 +/- 3.6 kcal/mol, which is in agreement with the value of 22.4 kcal/mol determined from the experimental rate constant (0.015 min(-1)). The third methylation [Lys27-N(Me)(2) + AdoMet -> Lys27-N(Me)(3)(+) + AdoHcy] is associated with a Delta G(double dagger) of 23.1 +/- 4.0 kcal/mol, which is in agreement with the value of 23.0 kcal/mol determined from the experimental rate constant (0.005 min(-1)). Our computations establish that the first, second, and third methyl transfer steps catalyzed by vSET are linear S(N)2 reactions with the bond making being similar to 50% associative.