Brand  (β version)

PDB ID: 2OT7

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Ligands
Code Name Style Show Link
NI Nickel (II) ion PoSSuM
ZN Zinc ion PoSSuM
OGA N-oxalylglycine PoSSuM
Non-standard Residues
Code Name Show
MLZ N-methyl-lysine
ALY N(6)-acetyllysine
Glycosylation
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Structure summary

Code : 2OT7   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE
Title : Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9
Release Data : 2007-03-13
Compound :
mol_id molecule chains synonym
1 JmjC domain-containing histone demethylation protein 3A A,B Jumonji domain-containing protein 2A
ec: 1.14.11.-
mol_id molecule chains
2 histone 3 K9 monomethyl C,D
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: JMJD2A, JHDM3A, JMJD2, KIAA0677
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pNIC28-Bsa4
mol_id organism_scientific
2
synthetic: yes
other_details: Synthetic H3 peptide monomethylated at K9. Its sequence is based on human histone H3 fragment (residues 7-14), gene HIST1H3A
Authors : Kavanagh, K.L., Ng, S.S., Pilka, E., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)
Keywords : Fe, double-stranded beta helix, demethylase, oxygenase, Structural Genomics, Structural Genomics Consortium, SGC, OXIDOREDUCTASE
Exp. method : X-RAY DIFFRACTION ( 2.135 Å )
Citation :

Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.

Ng, S.S.,Kavanagh, K.L.,McDonough, M.A.  et al.
(2007)  Nature  448 : 87 - 91

PubMed: 17589501
DOI: 10.1038/nature05971

Reaction

Chain : A, B
UniProt : O75164 (KDM4A_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 2 2- oxoglutarate + 2 O2 = N(6)-methyl-L-lysyl(9)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 1.14.11.66 PubMed:16603238
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N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3] + 2 2- oxoglutarate + 2 O2 = N(6)-methyl-L-lysyl(36)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 1.14.11.69 PubMed:16603238
-
Cofactor: Evidence: Note:
Fe(2+) ECO:0000269 | PubMed:16603238
Binds 1 Fe(2+) ion per subunit.