Mechanisms of Substrate Recognition by the Multispecific Protein Lysine Methyltransferase SETD6

The SETD6 protein lysine methyltransferase monomethylates specific lysine residues in a diverse set of substrates which contain the target lysine residue in a highly variable amino acid sequence context. To investigate the mechanism underlying this multispecificity, we analyzed SETD6 substrate recognition using AlphaFold 3 docking and peptide SPOT array methylation experiments. Structural modeling of the SETD6-E2F1 complex suggested that substrate binding alone is insufficient to restrict SETD6 activity to only one lysine residue, pointing to additional sequence readout at the target site. Methylation of mutational scanning peptide SPOT arrays derived from four different SETD6 substrates (E2F1 K117, H2A.Z K7, RELA K310, and H4 K12) revealed sequence preferences of SETD6 at positions -1, +2, and +3 relative to the target lysine. Notably, glycine or large aliphatic residues were favored at -1, isoleucine/valine at +2, and lysine at +3. These preferences, however, were sequence context dependent and variably exploited among different substrates, indicating conformational variability of the enzyme-substrate interface. Mutation of SETD6 residue L260, which forms a contact with the +2 site in the available SETD6-RELA structure, further demonstrated substrate-specific differences in recognition at the +2/+3 sites. Together, these findings reveal a versatile mode of peptide recognition in which the readout of each substrate position depends on the overall substrate peptide sequence. These findings can explain the multispecificity of SETD6 and similar mechanisms may underlie substrate selection in other protein methyltransferases.