› 4nii

X-ray diffraction
1.62Å resolution

Crystal structure of AlkB D135I mutant protein with cofactors bound to dsDNA containing m6A/A

Released:
DOI: 10.2210/pdb4nii/pdb
PDB entry 4nii coloured by chain, front view.
PDB entry 4nii coloured by chain, side view.
PDB entry 4nii coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues.
Zhu C, Yi C
Angew Chem Int Ed Engl 53 3659-62 (2014)
PMID: 24596302

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117876 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 205 amino acids
Theoretical weight: 22.83 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 1 x MN
Ligand AKG 1 x AKG
1 modified residue:
Ligand 6MA 1 x 6MA

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 41.374Å b: 75.902Å c: 52.285Å
α: 90° β: 108.6° γ: 90°
R-values:
R R work R free
0.176 0.174 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond.
Fedeles et al. (2015)
10 more