› 4gjz

X-ray diffraction
1.05Å resolution

JMJD5 in complex with 2-oxoglutarate

Released:
DOI: 10.2210/pdb4gjz/pdb
PDB entry 4gjz coloured by chain, front view.
PDB entry 4gjz coloured by chain, side view.
PDB entry 4gjz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and functional analysis of JMJD5 indicate an alternate specificity and function.
Del Rizzo PA, Krishnan S, Trievel RC
Mol Cell Biol 32 4044-52 (2012)
PMID: 22851697

Function and Biology Details

Reaction catalysed: 
[Protein]-L-arginine + 2-oxoglutarate + O(2) = [protein]-(3R)-3-hydroxy-L-arginine + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185372 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional peptidase and arginyl-hydroxylase JMJD5 Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 27.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8N371 (Residues: 183-416; Coverage: 56%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain
Structure domains: Cupin

Ligands and Environments

3 bound ligands:
Ligand CO 1 x CO
Ligand AKG 1 x AKG
Ligand BME 1 x BME
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 49.695Å b: 64.056Å c: 76.801Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.148 0.147 0.163
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Histone lysine demethylases as targets for anticancer therapy.
Højfeldt et al. (2013)
10 more

7 mentions without citation

Crystal structure and functional analysis of JMJD5 indicate an alternate specificity and function.
Del Rizzo et al. (2012)
6 more