› 3k3o

X-ray diffraction
2.1Å resolution

Crystal structure of the catalytic core domain of human PHF8 complexed with alpha-ketoglutarate

Released:
DOI: 10.2210/pdb3k3o/pdb
PDB entry 3k3o coloured by chain, front view.
PDB entry 3k3o coloured by chain, side view.
PDB entry 3k3o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into a novel histone demethylase PHF8.
Yu L, Wang Y, Huang S, Wang J, Deng Z, Zhang Q, Wu W, Zhang X, Liu Z, Gong W, Chen Z
Cell Res 20 166-73 (2010)
PMID: 20101266

Function and Biology Details

Reactions catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(36) + succinate + formaldehyde + CO(2)
(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

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194029 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone lysine demethylase PHF8 Chain: A
Molecule details ›
Chain: A
Length: 371 amino acids
Theoretical weight: 43.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UPP1 (Residues: 122-483; Coverage: 34%)
Gene names: KIAA1111, PHF8, ZNF422
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand AKG 1 x AKG
Ligand FE2 1 x FE2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 52.092Å b: 52.532Å c: 134.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.233
Expression system: Escherichia coli

Quick links

Citations

17 review citations

Molecular mechanisms and potential functions of histone demethylases.
Kooistra et al. (2012)
16 more

6 mentions without citation

Dynamics of histone lysine methylation: structures of methyl writers and erasers.
Upadhyay et al. (2011)
5 more