Double Specificity Of Histone Methylation Cekdm7a Enzyme Structure And Function Studies

Histone methylation, which occurs on both arginine and lysine residues, is recognized as an important epigenetic modification linked to heterochromatin formation, genomic imprinting and X-chromosome inactivation as well as DNA damage response. Although histone methylation was long considered irreversible, the recent identification of numerous site-specific histone demethylases provides compelling evidence that this modification is dynamically regulated. Till now, two distinct classes of demethylases have been characterized. The first class, represented by LSD1, uses FAD as a cofactor through an amine oxidate reaction to remove lysine methyl group. The second class is the family of JmjC-domain-containing demethylases, which require Fe(II) and a-ketoglutarate (a-KG) as cofactors in the demethylation process.Recently, we and our collaborator identified that ceKDM7A, a PHD and JmjC-domain-containing protein from C.elegans, is a histone demethylase specific for H3K9me2and H3K27me2, and the PDH finger binding to H3K4me3guides the demethylation activity in vivo. To provide structural insight into the molecular mechanism for ceKDM7A, we solved six crystal structures of the enzyme in apo form and in complex with single or two peptides containing various combinations of H3K4me3, H3K9me2and H3K27me2modifications. The structures indicated that H3K4me3binds to the PHD finger through β-augmentation, H3K9me2and H3K27me2interact with ceKDM7A in a similar fashion, and that the peptide-binding specificity is determined by a network of specific interactions. The geometrical measurement of the structures also revealed that H3K4me3associated with the PHD finger and H3K9me2bound to the JmjC domain are from two separate molecules, suggesting a trans-histone peptide-binding mechanism.In order to gain mechanistic insights of2-HG inhibition, we determined the structures both ceKDM7A bound with D-2-HG at2.1A and ceKDM7A bound with a-KG at2.25A. Comparison of these two structures reveals that2-HG occupies the same space as a-KG does in the active site of histone demethylases. These results not only provide a structural basis supporting D-2-HG as a competitor of a-KG, but also provide new ideas for tumor therapy and drug design.