› 4rfr

X-ray diffraction
1.5Å resolution

Complex structure of AlkB/rhein

Released:
DOI: 10.2210/pdb4rfr/pdb
PDB entry 4rfr coloured by chain, front view.
PDB entry 4rfr coloured by chain, side view.
PDB entry 4rfr coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage.
Li Q, Huang Y, Liu X, Gan J, Chen H, Yang CG
J Biol Chem 291 11083-93 (2016)
PMID: 27015802

Function and Biology Details

Reaction catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138340 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: B
Molecule details ›
Chain: B
Length: 203 amino acids
Theoretical weight: 22.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 14-216; Coverage: 94%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

2 bound ligands:
Ligand RHN 1 x RHN
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 36.95Å b: 39.2Å c: 40.521Å
α: 77.37° β: 74.67° γ: 65.47°
R-values:
R R work R free
0.119 0.118 0.15
Expression system: Escherichia coli

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Citations

21 review citations

The emerging roles of N6-methyladenosine (m6A) deregulation in liver carcinogenesis.
Chen et al. (2020)
20 more

2 mentions without citation

Targeting the RNA demethylase FTO for cancer therapy.
Zhou et al. (2021)
1 more