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2RFI

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide

Summary for 2RFI
Entry DOI10.2210/pdb2rfi/pdb
Related2IGQ
DescriptorHistone-lysine N-methyltransferase, H3 lysine-9 specific 5, Histone H3, ZINC ION, ... (5 entities in total)
Functional Keywordseuchromatic histone methyltransferase 1, structural genomics, structural genomics consortium, sgc, alternative splicing, ank repeat, chromatin regulator, nucleus, phosphorylation, polymorphism, s-adenosyl-l-methionine, acetylation, chromosomal protein, dna damage, dna repair, dna-binding, methylation, nucleosome core, transferase
Biological sourceHomo sapiens (human)
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Cellular locationNucleus: Q9H9B1
Total number of polymer chains4
Total formula weight69281.16
Authors
Min, J.,Wu, H.,Loppnau, P.,Weigelt, J.,Sundstrom, M.,Arrowsmith, C.H.,Edwards, A.M.,Bochkarev, A.,Plotnikov, A.N.,Structural Genomics Consortium (SGC) (deposition date: 2007-09-30, release date: 2007-10-23, Last modification date: 2023-08-30)
Primary citationWu, H.,Min, J.,Lunin, V.V.,Antoshenko, T.,Dombrovski, L.,Zeng, H.,Allali-Hassani, A.,Campagna-Slater, V.,Vedadi, M.,Arrowsmith, C.H.,Plotnikov, A.N.,Schapira, M.
Structural biology of human H3K9 methyltransferases
Plos One, 5:e8570-e8570, 2010
Cited by
PubMed Abstract: 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.
PubMed: 20084102
DOI: 10.1371/journal.pone.0008570
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.59 Å)
Structure validation

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数据于2025-07-23公开中

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