Catalytic mechanism and product specificity of Rubisco large subunit methyltransferase: QM/MM and MD investigations

Molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have been carried out in an investigation of Rubisco large subunit methyltransferase (LSMT). It was found that the appearance of a water channel is required for the stepwise methylation by S-adenosylmethionine (AdoMet). The water channel appears in the presence of AdoMet (LSMT center dot Lys-NH3+center dot AdoMet), but is not present immediately after methyl transfer (LSMT center dot Lys-N(Me)H-2(+)center dot AdoHcy). The water channel allows proton dissociation from both LSMT center dot AdoMet center dot Lys-NH3+ and LSMT center dot AdoMet center dot Lys-N(Me)H-2(+). The water channel does not appear for proton dissociation from LSMT center dot AdoMet center dot Lys-N(Me)(2)H+, and a third methyl transfer does not occur. By QM/MM, the calculated free energy barrier of the first methyl transfer reaction catalyzed by LSMT (Lys-NH2 + AdoMet -> Lys-N(Me)H-2(+) + AdoHcy) is Delta G(double dagger) = 22.8 +/- 3.3 kcal/mol. This Delta G(double dagger) is in remarkable agreement with the value 23.0 kcal/mol calculated from the experimental rate constant (6.2 x 10(-5) s(-1)). The calculated Delta G(double dagger) of the second methyl transfer reaction (AdoMet + Lys-N(Me)H -> AdoHcy + Lys-N(Me)(2)H+) at the QM/MM level is 20.5 +/- 3.6 kcal/mol, which is in agreement with the value 22.0 kcal/mol calculated from the experimental rate constant (2.5 x 10(-4) s(-1)). The third methyl transfer (Lys-N(Me)(2) + AdoMet -> Lys-N(Me)(3)(+) + AdoHcy) is associated with an allowed Delta G(double dagger) of 25.9 +/- 3.2 kcal/mol. However, this reaction does not occur because a water channel does not form to allow the proton dissociation of Lys-N(Me)(2)H+. Future studies will determine whether the product specificity of lysine (mono, di, and tri) methyltransferases is determined by the formation of water channels.