› 3kv5

X-ray diffraction
2.39Å resolution

Structure of KIAA1718, human Jumonji demethylase, in complex with N-oxalylglycine

Released:
DOI: 10.2210/pdb3kv5/pdb
PDB entry 3kv5 coloured by chain, front view.
PDB entry 3kv5 coloured by chain, side view.
PDB entry 3kv5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X
Nat Struct Mol Biol 17 38-43 (2010)
PMID: 20023638

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-180579 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 7A Chains: A, D
Molecule details ›
Chains: A, D
Length: 488 amino acids
Theoretical weight: 55.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6ZMT4 (Residues: 1-488; Coverage: 52%)
Gene names: JHDM1D, KDM7, KDM7A, KIAA1718
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand FE2 3 x FE2
Ligand SO4 2 x SO4
Ligand OGA 1 x OGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 62.7Å b: 125.6Å c: 206.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.245
Expression system: Escherichia coli

Quick links

Citations

82 review citations

Histone methylation: a dynamic mark in health, disease and inheritance.
Greer et al. (2012)
81 more

9 mentions without citation

Histone lysine methylation dynamics: establishment, regulation, and biological impact.
Black et al. (2012)
8 more