2GP5

Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate

Summary for 2GP5

• Entry DOI: 10.2210/pdb2gp5/pdb
• Related: 2GP3
• Descriptor: Jumonji domain-containing protein 2A, ZINC ION, FE (II) ION, ... (5 entities in total)
• Functional Keywords: beta barrel, zinc finger, metal binding protein
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: O75164
• Total number of polymer chains: 2
• Total formula weight: 81711.07

Authors

Chen, Z.,Zang, J.,Whetstine, J.,Hong, X.,Davrazou, F.,Kutateladze, T.G.,Simpson, M.,Dai, S.,Hagman, J.,Shi, Y.,Zhang, G. (deposition date: 2006-04-16, release date: 2006-05-23, Last modification date: 2024-02-14)

Primary citation

Chen, Z.,Zang, J.,Whetstine, J.,Hong, X.,Davrazou, F.,Kutateladze, T.G.,Simpson, M.,Mao, Q.,Pan, C.H.,Dai, S.,Hagman, J.,Hansen, K.,Shi, Y.,Zhang, G.
Structural insights into histone demethylation by JMJD2 family members
Cell(Cambridge,Mass.), 125:691-702, 2006

PubMed Abstract: Posttranslational modifications of histones regulate chromatin structure and gene expression. Histone demethylases, members of a newly emerging transcription-factor family, remove methyl groups from the lysine residues of the histone tails and thereby regulate the transcriptional activity of target genes. JmjC-domain-containing proteins have been predicted to be demethylases. For example, the JmjC-containing protein JMJD2A has been characterized as a H3-K9me3- and H3-K36me3-specific demethylase. Here, structures of the catalytic-core domain of JMJD2A with and without alpha-ketoglutarate in the presence of Fe2+ have been determined by X-ray crystallography. The structure of the core domain, consisting of the JmjN domain, the JmjC domain, the C-terminal domain, and a zinc-finger motif, revealed the unique elements that form a potential substrate binding pocket. Sited-directed mutagenesis in conjunction with demethylase activity assays allowed us to propose a molecular model for substrate selection by the JMJD2 histone demethylase family.

PubMed: 16677698
DOI: 10.1016/j.cell.2006.04.024

Experimental method

X-RAY DIFFRACTION (2.28 Å)