Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity

Abstract

Methylation of certain lysine residues in the N-terminal tails of core histone proteins in nucleosome is of fundamental importance in the regulation of chromatin structure and gene expression. Such histone modification is catalyzed by protein lysine methyltransferases (PKMTs). PKMTs contain a conserved SET domain in almost all of the cases and may transfer one to three methyl groups from S-adenosyl-L-methionine (AdoMet) to the -amino group of the target lysine residue. Here, quantum mechanical/molecular mechanical molecular dynamics and free-energy simulations are performed on human PKMT SET7/9 and its mutants to understand two outstanding questions for the reaction catalyzed by PKMTs: the mechanism for deprotonation of positively charged methyl lysine (lysine) and origin of product specificity. The results of the simulations suggest that Tyr-335 (an absolute conserved residue in PKMTs) may play the role as the general base for the deprotonation after dissociation of AdoHcy (S-adenosyl-L-homocysteine) and before binding of AdoMet. It is shown that conformational changes could bring Y335 to the target methyl lysine (lysine) for proton abstraction. This mechanism provides an explanation why methyl transfers could be catalyzed by PKMTs processively. The freeenergy profiles for methyl transfers are reported and analyzed for wild type and certain mutants (Y305F and Y335F) and the activesite interactions that are of importance for the enzyme's function are discussed. The results of the simulations provide important insights into the catalytic process and lead to a better understanding of experimental observations concerning the origin of product specificity for PKMTs.enzyme catalysis ͉ quantum mechanical/molecular mechanical molecular dynamics simulations ͉ potential of mean force

Structural origins for the product specificity of SET domain protein methyltransferases

“…Conversely, a series of simulations with multiple SET domain PKMTs show that solvent chains are responsible for deprotonating the lysine -amine to promote methyltransfer (23)(24)(25)(26)(27), whereas the results of another modeling study of SET7/9 implicate the invariant active site tyrosine (Tyr-335; Figs. S1 and S2) as the catalytic base in deprotonation (28). Although there is no experimental data for solvent chains in our SET8 structures or in other SET domain PKMTs, it is conceivable that these chains could form transiently in solution to provide a deprotonation path during catalysis, in agreement with our model (see below).…”

Molecular basis for histone N-terminal methylation by NRMT1

“…4B), which can serve as an ideal path for the release of protons generated by the methyl transfer reaction (Hammes-Schiffer and Tully 1994). The S N 2 reaction has been proposed as a common mechanism for SAM-MTase, in which the methyl-acceptor group is deprotonated usually by a general base in the first position (Guo and Guo 2007). However, we were not able to identify any adjacent acidic or proton acceptor residue that may directly deprotonate the α-amino of CENP-A.…”

Chemical mechanisms of histone lysine and arginine modifications

“…These interactions position AdoMet in a U-shaped conformation that places the methylsulfonium group at the base of a hydrophobic channel in which the lysine substrate binds. In Set7/9, the side chain hydroxyls of Tyr-245 and Tyr-305 hydrogen bond to the ε-amine of lysine, directing the lone pair towards the methyl group of AdoMet [18]. The AdoMet methyl group is positioned and activated by C-H … O hydrogen bonds between the methyl group and the side chain hydroxyl of Tyr-335 and the main chain carboxyls of Gly-264 and His-293.…”