2YBS image
Entry Detail
PDB ID:
2YBS
Title:
JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2011-03-10
Release Date:
2011-03-30
Method Details:
Experimental Method:
Resolution:
2.32 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:LYSINE-SPECIFIC DEMETHYLASE 4A
Chain IDs:A, B
Chain Length:381
Number of Molecules:2
Biological Source:HOMO SAPIENS
Polymer Type:polypeptide(L)
Description:HISTONE H3.1T
Chain IDs:C, D
Chain Length:12
Number of Molecules:2
Biological Source:HOMO SAPIENS
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
M3L C LYS N-TRIMETHYLLYSINE
Primary Citation
The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
EMBO Rep. 12 463 469 (2011)
PMID: 21460794 DOI: 10.1038/embor.2011.43

Abstact

Mutations in isocitrate dehydrogenases (IDHs) have a gain-of-function effect leading to R(-)-2-hydroxyglutarate (R-2HG) accumulation. By using biochemical, structural and cellular assays, we show that either or both R- and S-2HG inhibit 2-oxoglutarate (2OG)-dependent oxygenases with varying potencies. Half-maximal inhibitory concentration (IC(50)) values for the R-form of 2HG varied from approximately 25 μM for the histone N(ɛ)-lysine demethylase JMJD2A to more than 5 mM for the hypoxia-inducible factor (HIF) prolyl hydroxylase. The results indicate that candidate oncogenic pathways in IDH-associated malignancy should include those that are regulated by other 2OG oxygenases than HIF hydroxylases, in particular those involving the regulation of histone methylation.

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Primary Citation of related structures