» Articles » PMID: 20084102

Structural Biology of Human H3K9 Methyltransferases

Abstract

Unlabelled: 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.

Enhanced Version: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Citing Articles

The function of histone methyltransferase SETDB1 and its roles in liver cancer.

Zhang E, He P Front Cell Dev Biol. 2024; 12:1500263.

PMID: 39583200 PMC: 11582049. DOI: 10.3389/fcell.2024.1500263.


Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome.

Rots D, Bouman A, Yamada A, Levy M, Dingemans A, de Vries B Am J Hum Genet. 2024; 111(8):1605-1625.

PMID: 39013458 PMC: 11339614. DOI: 10.1016/j.ajhg.2024.06.008.


G9a in Cancer: Mechanisms, Therapeutic Advancements, and Clinical Implications.

Ni Y, Shi M, Liu L, Lin D, Zeng H, Ong C Cancers (Basel). 2024; 16(12).

PMID: 38927881 PMC: 11201431. DOI: 10.3390/cancers16122175.


SETDB1 as a cancer target: challenges and perspectives in drug design.

Hassanie H, Penteado A, de Almeida L, Calil R, da Silva Emery F, Costa-Lotufo L RSC Med Chem. 2024; 15(5):1424-1451.

PMID: 38799223 PMC: 11113007. DOI: 10.1039/d3md00366c.


Writers and readers of H3K9me2 form distinct protein networks during the cell cycle that include candidates for H3K9 mimicry.

Pollin G, de Assuncao T, Jorge S, Chi Y, Charlesworth M, Madden B Biosci Rep. 2023; 43(10).

PMID: 37782747 PMC: 10611923. DOI: 10.1042/BSR20231093.


References
1.
Couture J, Dirk L, Brunzelle J, Houtz R, Trievel R . Structural origins for the product specificity of SET domain protein methyltransferases. Proc Natl Acad Sci U S A. 2008; 105(52):20659-64. PMC: 2634886. DOI: 10.1073/pnas.0806712105. View

2.
Copeland R, Solomon M, Richon V . Protein methyltransferases as a target class for drug discovery. Nat Rev Drug Discov. 2009; 8(9):724-32. DOI: 10.1038/nrd2974. View

3.
Dillon S, Zhang X, Trievel R, Cheng X . The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol. 2005; 6(8):227. PMC: 1273623. DOI: 10.1186/gb-2005-6-8-227. View

4.
Xiao B, Wilson J, Gamblin S . SET domains and histone methylation. Curr Opin Struct Biol. 2003; 13(6):699-705. DOI: 10.1016/j.sbi.2003.10.003. View

5.
Couture J, Collazo E, Brunzelle J, Trievel R . Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Genes Dev. 2005; 19(12):1455-65. PMC: 1151662. DOI: 10.1101/gad.1318405. View