8z7e

Structure of G9a in complex with compound 9b

Structural highlights

8z7e is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.545Å
Ligands:	A1L09, SFG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EHMT2_HUMAN Histone methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting HP1 proteins to methylated histones. Also mediates monomethylation of 'Lys-56' of histone H3 (H3K56me1) in G1 phase, leading to promote interaction between histone H3 and PCNA and regulating DNA replication. Also weakly methylates 'Lys-27' of histone H3 (H3K27me). Also required for DNA methylation, the histone methyltransferase activity is not required for DNA methylation, suggesting that these 2 activities function independently. Probably targeted to histone H3 by different DNA-binding proteins like E2F6, MGA, MAX and/or DP1. May also methylate histone H1. In addition to the histone methyltransferase activity, also methylates non-histone proteins: mediates dimethylation of 'Lys-373' of p53/TP53. Also methylates CDYL, WIZ, ACIN1, DNMT1, HDAC1, ERCC6, KLF12 and itself.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The discovery and development of structurally distinct lysine methyltransferase G9a inhibitors have been the subject of intense research in epigenetics. Structure-based optimization was conducted, starting with the previously reported seed compound 7a and lead to the identification of a highly potent G9a inhibitor, compound 7i (IC(50) = 0.024 muM). X-ray crystallography for the ligand-protein interaction and kinetics study, along with surface plasmon resonance (SPR) analysis, revealed that compound 7i interacts with G9a in a unique binding mode. In addition, compound 7i caused attenuation of cellular H3K9me2 levels and induction of gamma-globin mRNA expression in HUDEP-2 cells in a dose-dependent manner.

Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment.,Nishigaya Y, Takase S, Sumiya T, Sato T, Niwa H, Sato S, Nakata A, Matsuoka S, Maemoto Y, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F Bioorg Med Chem Lett. 2024 Sep 15;110:129856. doi: 10.1016/j.bmcl.2024.129856. , Epub 2024 Jun 22. PMID:38914346^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Milner CM, Campbell RD. The G9a gene in the human major histocompatibility complex encodes a novel protein containing ankyrin-like repeats. Biochem J. 1993 Mar 15;290 ( Pt 3):811-8. PMID:8457211
↑ Tachibana M, Sugimoto K, Fukushima T, Shinkai Y. Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem. 2001 Jul 6;276(27):25309-17. Epub 2001 Apr 20. PMID:11316813 doi:10.1074/jbc.M101914200
↑ Rathert P, Dhayalan A, Murakami M, Zhang X, Tamas R, Jurkowska R, Komatsu Y, Shinkai Y, Cheng X, Jeltsch A. Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol. 2008 Jun;4(6):344-6. doi: 10.1038/nchembio.88. Epub 2008 Apr 27. PMID:18438403 doi:10.1038/nchembio.88
↑ Huang J, Dorsey J, Chuikov S, Zhang X, Jenuwein T, Reinberg D, Berger SL. G9A and GLP methylate lysine 373 in the tumor suppressor p53. J Biol Chem. 2010 Jan 29. PMID:20118233 doi:M109.062588
↑ Yu Y, Song C, Zhang Q, DiMaggio PA, Garcia BA, York A, Carey MF, Grunstein M. Histone H3 lysine 56 methylation regulates DNA replication through its interaction with PCNA. Mol Cell. 2012 Apr 13;46(1):7-17. doi: 10.1016/j.molcel.2012.01.019. Epub 2012, Mar 1. PMID:22387026 doi:10.1016/j.molcel.2012.01.019
↑ Nishigaya Y, Takase S, Sumiya T, Sato T, Niwa H, Sato S, Nakata A, Matsuoka S, Maemoto Y, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F. Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment. Bioorg Med Chem Lett. 2024 Sep 15;110:129856. PMID:38914346 doi:10.1016/j.bmcl.2024.129856

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Milner CM, Campbell RD. The G9a gene in the human major histocompatibility complex encodes a novel protein containing ankyrin-like repeats. Biochem J. 1993 Mar 15;290 ( Pt 3):811-8. PMID:8457211

[2] Tachibana M, Sugimoto K, Fukushima T, Shinkai Y. Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem. 2001 Jul 6;276(27):25309-17. Epub 2001 Apr 20. PMID:11316813 doi:10.1074/jbc.M101914200

[3] Rathert P, Dhayalan A, Murakami M, Zhang X, Tamas R, Jurkowska R, Komatsu Y, Shinkai Y, Cheng X, Jeltsch A. Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol. 2008 Jun;4(6):344-6. doi: 10.1038/nchembio.88. Epub 2008 Apr 27. PMID:18438403 doi:10.1038/nchembio.88

[4] Huang J, Dorsey J, Chuikov S, Zhang X, Jenuwein T, Reinberg D, Berger SL. G9A and GLP methylate lysine 373 in the tumor suppressor p53. J Biol Chem. 2010 Jan 29. PMID:20118233 doi:M109.062588

[5] Yu Y, Song C, Zhang Q, DiMaggio PA, Garcia BA, York A, Carey MF, Grunstein M. Histone H3 lysine 56 methylation regulates DNA replication through its interaction with PCNA. Mol Cell. 2012 Apr 13;46(1):7-17. doi: 10.1016/j.molcel.2012.01.019. Epub 2012, Mar 1. PMID:22387026 doi:10.1016/j.molcel.2012.01.019

[6] Nishigaya Y, Takase S, Sumiya T, Sato T, Niwa H, Sato S, Nakata A, Matsuoka S, Maemoto Y, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F. Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment. Bioorg Med Chem Lett. 2024 Sep 15;110:129856. PMID:38914346 doi:10.1016/j.bmcl.2024.129856

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8z7e

Structure of G9a in complex with compound 9b

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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