Structural Biology of Human H3K9 Methyltransferases
SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity. Post-translational modifications of histone proteins regulate chromatin compaction, mediate epigenetic regulation of transcription, and control cellular differentiation in health and disease. Methylation of histone tails is one of the fundamental events of epigenetic signaling. Tri-methylation of lysine 9 of histone 3 (H3K9) mediates chromatin recruitment of HP1, heterochromatin condensation and gene silencing. Similarly, methylation of H3K27 and H4K20 are associated with a repressed state of chromatin, whereas expressed genes are methylated at H3K4, H3K36 and H3K79. Histone methyltransferases are divided into protein arginine methyltransferases (PRMTs) and histone lysine methyltransferases (HKMTs). HKMTs catalyze the transfer of a methyl group from the co-factor S-adenosyl-L-methionine (SAM) to a substrate lysine and, with the exception of DOT1L, are all organized around a canonical SET domain. The structures of a number of HKMTs have been reported, including ternary complexes of human orthologs with co-factor and substrate peptides (SETD7-H3K4, SETD8-H4K20 and MLL1-H3K4), as well as N. crassa Dim-5 in complex with a H3K9 peptide and a viral protein complexed to H3K27. These structures collectively highlighted a remarkable plasticity of the peptide-binding site and a lack of clear structural motifs that correlate with sequence selectivity. Methylation of H3K9 in humans relies mostly on members of the Suv39 family, namely EHMT1/GLP, EHMT2/G9a, SUV39H1, SUV39H2, SETDB1 and SETDB2, as well as then non-Suv39 enzymes PRDM2 and ASH1L. Here we report the high-resolution crystal structures of the methyltransferase domains of GLP, G9a, SUV39H2 and PRDM2, and propose a structural mechanism for substrate recognition. Our data also provide important insight to guide the development of potent and selective inhibitors of HKMTs, which are likely to have applications in a variety of diseases including regenerative medicine, oncology and inflammation.
- Research Organization:
- Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source
- Sponsoring Organization:
- DOE - OFFICE OF SCIENCE
- DOE Contract Number:
- DE-AC02-98CH10886
- OSTI ID:
- 1019599
- Report Number(s):
- BNL-96015-2011-JA; TRN: US201115%%240
- Journal Information:
- PLoS One, Vol. 5, Issue 1
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ARGININE
BIOLOGY
CHROMATIN
CRYSTAL STRUCTURE
DISEASES
ELECTROSTATICS
ENZYMES
GENES
HETEROCHROMATIN
HISTONES
INFLAMMATION
LYSINE
MEDICINE
METHYLATION
MUTANTS
PEPTIDES
PLASTICITY
PROTEINS
RESIDUES
SUBSTRATES
TRANSCRIPTION
national synchrotron light source