Characterisation of protein methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 reveals extensive post-translational modification

Protein methylation is one of the major post-translational modifications (PTMs) in the cell. In Saccharomyces cerevisiae, over twenty protein methyltransferases (MTases) and their respective substrates have been identified. However, the way in which these MTases are modified, and potentially subject to regulation, remains poorly understood. Here, we investigated six S. cerevisiae protein MTases (Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1) to identify PTMs of potential functional relevance. We identified 51 PTM sites across the six MTases, including phosphorylation, acetylation and methylation. 45 sites are novel. We contextualised the PTM sites in structural models of the MTases and revealed that many fell in catalytic pockets or enzyme-substrate interfaces. These may regulate MTase activity. Finally, we compared PTMs on Hmt1 with those on its human homologs PRMT1, PRMT3, CARM1, PRMT6 and PRMT8. This revealed that several PTMs are conserved from yeast to human, whereas others are only found in Hmt1.