Molecular basis for the methylation specificity of ATXR5 for histone H3

Nucleic Acids Res. 2017 Jun 20;45(11):6375-6387. doi: 10.1093/nar/gkx224.


In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.

MeSH terms

  • Amino Acid Motifs
  • Arabidopsis / enzymology*
  • Arabidopsis Proteins / chemistry*
  • Arabidopsis Proteins / physiology
  • Catalytic Domain
  • Crystallography, X-Ray
  • Gene Expression Regulation, Plant
  • Histones / chemistry*
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Methylation
  • Methyltransferases / chemistry*
  • Methyltransferases / physiology
  • Models, Molecular
  • Protein Binding
  • Protein Processing, Post-Translational
  • Substrate Specificity


  • Arabidopsis Proteins
  • Histones
  • ATXR5 protein, Arabidopsis
  • Methyltransferases