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

  • ️Mon Jan 01 2007

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

Hao-Bo Guo et al. Proc Natl Acad Sci U S A. 2007.

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 epsilon-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 free-energy profiles for methyl transfers are reported and analyzed for wild type and certain mutants (Y305F and Y335F) and the active-site 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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.

The methyl transfer reaction catalyzed by SET7/9 and active site structures obtained from the simulations. (A) A methyl group is transferred from AdoMet to H3-K4, leading to the formation of a monomethylated lysine product (H3-K4me). (B) The relative orientation of AdoMet and H3-K4 in the reactant complex. The efficiency of the methyl transfer depends on the values of r(CM… Nζ) and θ in the reactant complexes. θ is defined as the angle between the two vectors r1 and r2. Here, r1 is the direction of the lone pair of electrons on Nζ, and r2 is the vector pointing from CM to Sδ. (C) An average active-site structure obtained from the QM/MM MD simulations of SET7/9 complexed with AdoMet and a histone H3-K4 peptide along with two-dimensional plot of r(CM… Nζ) and θ distributions from the 1-ns MD simulations. SET7/9 is shown in balls and sticks, and AdoMet and H3-K4 are in sticks. The distances are in angstroms. The free-energy changes as functions of r(CM… Nζ) and θ obtained based on the distributions are given in SI Fig. 5A. (D) The average active-site structure in the area near the transition state of monomethylation in wild type obtained based on the free-energy simulations (see below).

Fig. 2.
Fig. 2.

The free-energy changes for the first methyl transfer from AdoMet to H3-K4 and the second methyl transfer from AdoMet to H3-K4me as a function of the reaction coordinate [R = r(CM… Sδ) − r(CM… Nζ)] in wild type and certain mutants. (A) Wild type. Solid line, the first methyl transfer; dotted line, the second methyl transfer. (B) Y305F and Y335F. Solid line, the first methyl transfer in Y305F; dotted line, the second methyl transfer in Y305F; dashed line, the first methyl transfer in Y335F.

Fig. 3.
Fig. 3.

The average structures of the reactant complexes of Y305F and Y335F from the simulations. (A) Y305F complexed with AdoMet and H3-K4. (B) Wild type complexed with AdoMet and H3-K4me along with the r(CM… Nζ) and θ distributions. (C) Y305F complexed with AdoMet and H3-K4me along with the r(CM… Nζ) and θ distributions. (D) Y335F complexed with AdoMet and H3-K4.

Fig. 4.
Fig. 4.

Proton abstraction from H3-K4me by Y335 in the Y305F mutant. (A) The average structure of Y305F complexed with the positively charged H3-K4me without the cofactor. The conserved hydrogen bond between Tyr-335 and the backbone carboxyl oxygen of Ala-295 was broken, and the hydroxyl group of Tyr-335 donates a hydrogen bond to bulk water molecules instead. (B) The distance between the Tyr-335 oxygen and the proton of H3-K4me as a function of time during the MD simulations. This plot shows that, when Y335 is deprotonated, it undergoes conformational changes and abstracts a proton from the positively charged H3-K4me. (C) The average structure from the MD simulations after Tyr-335 abstracted the proton from H3-K4me. Two hydrogen bonds observed in the crystal structure involving Tyr-245 (with H3-K4me) and Tyr-335 (with the carbonyl oxygen of Ala-295) are recovered. (D) The mechanism of deprotonation of methyl lysine proposed from this study.

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