Mechanism of product specificity of AdoMet methylation catalyzed by lysine methyltransferases: transcriptional factor p53 methylation by histone lysine methyltransferase SET7/9.
The catalysis by SET7/9 histone lysine methyltransferase of AdoMet N-methylation of the transcriptional factor p53-Lys4-NH 2 has been investigated with particular attention paid to the means of product specificity. After formation of the SET7/9.p53-Lys4-NH 3 (+).AdoMet complex, the following events occur: (i) the appearance of a water channel, (ii) a depronation of p53-Lys4-NH 3 (+) via this water channel into the aqueous solvent, and (iii) AdoMet methylation of p53-Lys4-NH 2 to form p53-Lys4-N(Me)H 2 (+). The formation of a water channel does not occur on formation of the SET7/9.p53-Lys4-NH 3 (+), SET7/9.p53-Lys4-N(Me)H 2 (+).AdoHcy, or SET7/9.p53-Lys4-N(Me)H 2 (+).AdoMet complex. Without a water channel, the substrate p53-Lys4-N(Me)H is not available because the proton dissociation p53-Lys4-N(Me)H 2 (+) --> p53-Lys4-N(Me)H + H (+) does not occur. The lack of formation of a water channel is due to the positioning of the methyl substituent of the SET7/9.p53-Lys4-N(Me)H 2 (+).AdoMet complex. By quantum mechanics/molecular mechanics, the computed free energy barrier of the methyl transfer reaction [p53-Lys4-NH 2 + AdoMet --> p53-Lys4-N(Me)H 2 (+) + AdoHcy] in the SET7/9 complex is Delta G (++) = 20.1 +/- 2.9 kcal/mol. This Delta G (++) is in agreement with the value of 20.9 kcal/mol calculated from the experimental rate constant (1.2 +/- 0.1 min (-1)). Our bond-order computations establish that the methyl transfer reaction in protein lysine methyltransferases occurs via a linear S N2 associative reaction with bond making of approximately 50%.
Zhang
Xiaodong
X
Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
Bruice
Thomas C
TC
D001665:Binding Sites; D011495:Histone-Lysine N-Methyltransferase / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D008745:Methylation; D008956:Models, Chemical; D015394:Molecular Structure; D013379:Substrate Specificity; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry / Q000378:metabolism*
D016159:Tumor Suppressor Protein p53; D011495:Histone-Lysine N-Methyltransferase