› 3opt

X-ray diffraction
2.2Å resolution

Crystal structure of the Rph1 catalytic core with a-ketoglutarate

Released:
DOI: 10.2210/pdb3opt/pdb
PDB entry 3opt coloured by chain, front view.
PDB entry 3opt coloured by chain, side view.
PDB entry 3opt coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.
Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J
Biochem J 433 295-302 (2011)
PMID: 21067515

Function and Biology Details

Reaction 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)
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-153985 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA damage-responsive transcriptional repressor RPH1 Chain: A
Molecule details ›
Chain: A
Length: 373 amino acids
Theoretical weight: 43.61 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P39956 (Residues: 1-373; Coverage: 47%)
Gene names: RPH1, YER169W
Sequence domains:
Structure domains: Cupin

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P64
Unit cell:
a: 109.415Å b: 109.415Å c: 145.958Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.198 0.236
Expression system: Escherichia coli

Quick links

Citations

12 citation in other articles

The Histone H3K4 Demethylase JMJ16 Represses Leaf Senescence in Arabidopsis.
Liu et al. (2019)
11 more

5 mentions without citation

Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses.
Gao et al. (2018)
4 more