Substrate Specificity of the HEMK2 Protein Glutamine Methyltransferase and Identification of Novel Substrates

J Biol Chem. 2016 Mar 18;291(12):6124-33. doi: 10.1074/jbc.M115.711952. Epub 2016 Jan 21.

Abstract

Bacterial HEMK2 homologs initially had been proposed to be involved in heme biogenesis or to function as adenine DNA methyltransferase. Later it was shown that this family of enzymes has protein glutamine methyltransferase activity, and they methylate the glutamine residue in the GGQ motif of ribosomal translation termination factors. The murine HEMK2 enzyme methylates Gln(185) of the eukaryotic translation termination factor eRF1. We have employed peptide array libraries to investigate the peptide sequence recognition specificity of murine HEMK2. Our data show that HEMK2 requires a GQX3R motif for methylation activity. In addition, amino acid preferences were observed between the -3 and +7 positions of the peptide substrate (considering the target glutamine as 0), including a preference for Ser, Arg, and Gly at the +1 and a preference for Arg at the +7 position. Based on our specificity profile, we identified several human proteins that contain putative HEMK2 methylation sites and show that HEMK2 methylates 58 novel peptide substrates. After cloning, expression, and purification of the corresponding protein domains, we confirmed methylation for 11 of them at the protein level. Transfected CHD5 (chromodomain helicase DNA-binding protein 5) and NUT (nuclear protein in testis) were also demonstrated to be methylated by HEMK2 in human HEK293 cells. Our data expand the range of proteins potentially subjected to glutamine methylation significantly, but further investigation will be required to understand the function of HEMK2-mediated methylation in proteins other than eRF1.

Keywords: S-adenosylmethionine (SAM); enzyme; enzyme catalysis; enzyme specificity; methylglutamine; post-translational modification (PTM); protein methylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • DNA Helicases / metabolism
  • HEK293 Cells
  • Humans
  • Methylation
  • Mice
  • Nerve Tissue Proteins / metabolism
  • Nuclear Proteins / metabolism
  • Oncogene Proteins / metabolism
  • Protein Processing, Post-Translational*
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / chemistry*
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / physiology
  • Substrate Specificity

Substances

  • NUT protein, human
  • Nerve Tissue Proteins
  • Nuclear Proteins
  • Oncogene Proteins
  • PRED28 protein, mouse
  • Site-Specific DNA-Methyltransferase (Adenine-Specific)
  • DNA Helicases
  • CHD5 protein, human