Substrate and product specificities of SET domain methyltransferases

Abstract

SET domain lysine methyltransferases (KMTs) catalyze the site- and state-specific methylation of lysine residues in histone and non-histone substrates. These modifications play fundamental roles in transcriptional regulation, heterochromatin formation, X chromosome inactivation and DNA damage response, and have been implicated in the epigenetic regulation of cell identity and fate. The substrate and product specificities of SET domain KMTs are pivotal to eliciting these effects due to the distinct functions associated with site and state-specific protein lysine methylation. Here, we review advances in understanding the molecular basis of these specificities gained through structural and biochemical studies of the human methyltransferases Mixed Lineage Leukemia 1 (MLL1, also known as KMT2A) and SET7/9 (KMT7). We conclude by exploring the broader implications of these findings on the biological functions of protein lysine methylation by SET domain KMTs.

Figure 1

Crystal structure of the catalytic domain of human MLL1 bound to AdoHcy and a histone H3 dimethylated Lys-4 (H3K4me2) peptide at 2.2 Å resolution. (A) Ribbon diagram of the catalytic domain of MLL1 with the N-terminal SET (nSET; red), SET (gray), inserted SET (iSET; green) and PostSET (blue) domains denoted (PDB accession code 2W5Z). The PostSET Zn atom (gray sphere) and its coordinating cysteine residues are also illustrated. The H3K4me2 peptide and the product cofactor AdoHcy are depicted in stick representation with gold and green carbon atoms, respectively. The N- and C-termini of the MLL1 catalytic domain are also denoted. Several of the residues in the H3K4me2 peptide adopt alternative conformation. For clarity, these residues are rendered in one conformation. (B) Active site of MLL1 bound to K4me2 and AdoHcy. Residues in the enzyme and ligands are colored as in (A), and hydrogen bonds are shown as orange dashed lines. The Phe/Tyr switch residue Tyr-3942 is highlighted in magenta.

Figure 2

Substrate specificity of SET7/9. (A) Sequence alignment of the methylation sites of SET7/9 substrates. The methylated lysine is highlighted by white text on a black background and flanking residues that are conserved in at least half of the sequences are depicted with a gray background. The numbers at the top of the alignment denote the relative position of the residues in the methylation sites with respect to the target lysine (position 0). The predicted consensus sequence is shown at the bottom of the alignment and is based on the upper eight methylation sites. (B) The structure of the catalytic domain of human SET7/9 bound to a monomethylated TAF10 peptide (yellow carbon atoms) and AdoHcy (green carbons) at 1.3 Å resolution (PDB accession code 2F69). Positions of the consensus sequence in the TAF10 peptide are indicated by integers. The SET, the nSET, iSET and cSET domains in SET7/9 are colored gray, red, green and blue respectively. The dashed line represents the connectivity of the backbone for amino acids that were not resolved in the crystal structure.