2OT7: Crystal Structure Of Jmjd2a Complexed With Histone H3 Peptide Monomethylated At Lys9

Post-translational histone modification has a fundamental role in chromatin biology and is proposed to constitute a 'histone code' in epigenetic regulation. Differential methylation of histone H3 and H4 lysyl residues regulates processes including heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair and transcriptional regulation. The discovery of lysyl demethylases using flavin (amine oxidases) or Fe(II) and 2-oxoglutarate as cofactors (2OG oxygenases) has changed the view of methylation as a stable epigenetic marker. However, little is known about how the demethylases are selective for particular lysyl-containing sequences in specific methylation states, a key to understanding their functions. Here we reveal how human JMJD2A (jumonji domain containing 2A), which is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), discriminates between methylation states and achieves sequence selectivity for H3K9. We report structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. We propose a mechanism for achieving methylation state selectivity involving the orientation of the substrate methyl groups towards a ferryl intermediate. The results suggest distinct recognition mechanisms in different demethylase subfamilies and provide a starting point to develop chemical tools for drug discovery and to study and dissect the complexity of reversible histone methylation and its role in chromatin biology.
PDB ID: 2OT7Download
MMDB ID: 45258
PDB Deposition Date: 2007/2/7
Updated in MMDB: 2007/11
Experimental Method:
x-ray diffraction
Resolution: 2.13  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2OT7: dimeric; determined by author
Molecular Components in 2OT7
Label Count Molecule
Proteins (2 molecules)
Jmjc Domain-containing Histone Demethylation Protein 3A(Gene symbol: KDM4A)
Molecule annotation
Histone 3 K9 Monomethyl
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB