Histone Lysine Methyltransferase SET7/9: Formation of a Water Channel Precedes Each Methyl Transfer

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Abstract
Molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have been carried out in an investigation of histone lysine methyltransferase (SET7/9). Proton dissociation (SET7/9·Lys4-NH3+·AdoMet → SET7/9·Lys4-NH2·AdoMet + H+) must be prior to the methylation by S-adenosylmethionine (AdoMet). We find that a water channel is formed to allow escape of the proton to solvent. The water channel appears in the presence of AdoMet, but is not present in the species SET7/9·Lys4-NH3+ or SET7/9·Lys4-N(Me)H2+·AdoHcy. A water channel is not formed in the ground state of SET7/9·Lys4-N(Me)H2+·AdoMet, and the second methyl transfer does not occur. The structure of SET7/9·Lys4-N(Me)H2+·AdoMet includes a greater distance (6.1 ± 0.3 Å) between Cγ(AdoMet) and N(MeLys4) than is present in SET7/9·Lys4-NH3+·AdoMet (5.7 ± 0.2 Å). The electrostatic interactions between the positive charges on AdoMet and SET7/9·Lys4-NH3+ decrease the pKa of the latter from 10.9 ± 0.4 to 8.2 ± 0.6, and this is not seen in the SET7/9·Lys4-N(Me)H2+·AdoMet species. The formation, or not, of a water channel, the distance between Sδ(AdoMet) and N(Lys4), and the angle Sδ(AdoMet)−Cγ(AdoMet)−N(Lys4) determine whether methyl transfer can occur. By QM/MM, the calculated free energy barrier of the methyl transfer reaction in the SET7/9 [Lys4-NH2 + AdoMet → Lys4-N(Me)H2+ + AdoHcy] complex is ΔG⧧ = 19.0 ± 1.6 kcal/mol. This ΔG⧧ is in agreement with the value of 20.9 kcal/mol calculated from the experimental rate constant (0.24 min-1).