3N9P

ceKDM7A from C.elegans, complex with H3K4me3K27me2 peptide and NOG

Summary for 3N9P

• Entry DOI: 10.2210/pdb3n9p/pdb
• Related: 3N9L 3N9M 3N9N 3N9O 3N9Q
• Descriptor: Putative uncharacterized protein, Histone H3 peptide, FE (II) ION, ... (6 entities in total)
• Functional Keywords: histone, methylation, demethylase, phd, jmjc, fe(ii) and alpha-kg (alpha-ketoglutarate)-dependent dioxygenase family, oxidoreductase
• Biological source: Caenorhabditis elegans; More
• Cellular location: Nucleus: Q9GYI0 P08898
• Total number of polymer chains: 3
• Total formula weight: 69085.27

Authors

Yang, Y.,Hu, L.,Wang, P.,Hou, H.,Chen, C.D.,Xu, Y. (deposition date: 2010-05-31, release date: 2010-06-30, Last modification date: 2023-11-01)

Primary citation

Yang, Y.,Hu, L.,Wang, P.,Hou, H.,Lin, Y.,Liu, Y.,Li, Z.,Gong, R.,Feng, X.,Zhou, L.,Zhang, W.,Dong, Y.,Yang, H.,Lin, H.,Wang, Y.,Chen, C.D.,Xu, Y.
Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans
Cell Res., 20:886-898, 2010

PubMed Abstract: Histone lysine methylation can be removed by JmjC domain-containing proteins in a sequence- and methylation-state-specific manner. However, how substrate specificity is determined and how the enzymes are regulated were largely unknown. We recently found that ceKDM7A, a PHD- and JmjC domain-containing protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD finger binding to H3K4me3 guides the demethylation activity in vivo. To provide structural insight into the molecular mechanisms for the enzymatic activity and the function of the PHD finger, we solved six crystal structures of the enzyme in apo form and in complex with single or two peptides containing various combinations of H3K4me3, H3K9me2, and H3K27me2 modifications. The structures indicate that H3K9me2 and H3K27me2 interact 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 H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are from two separate molecules, suggesting a trans-histone peptide-binding mechanism. Thus, our systemic structural studies reveal not only the substrate recognition by the catalytic domain but also more importantly, the molecular mechanism of dual specificity of ceDKM7A for both H3K9me2 and H3K27me2.

PubMed: 20567261
DOI: 10.1038/cr.2010.86

Experimental method

X-RAY DIFFRACTION (2.388 Å)