› 3vk7

X-ray diffraction
2.1Å resolution

Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil

Released:
DOI: 10.2210/pdb3vk7/pdb
PDB entry 3vk7 coloured by chain, front view.
PDB entry 3vk7 coloured by chain, side view.
PDB entry 3vk7 coloured by chain, top view.
Source organism: Acanthamoeba polyphaga mimivirus
Primary publication:
Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA.
Imamura K, Averill A, Wallace SS, Doublié S
J Biol Chem 287 4288-98 (2012)
PMID: 22170059

Function and Biology Details

Reactions catalysed: 
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117057 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Probable formamidopyrimidine-DNA glycosylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 295 amino acids
Theoretical weight: 34.58 KDa
Source organism: Acanthamoeba polyphaga mimivirus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5UQ00 (Residues: 1-287; Coverage: 100%)
Gene name: MIMI_L315
Sequence domains:
Structure domains:
DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4.06 KDa
Source organism: Acanthamoeba polyphaga mimivirus
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 13 nucleotides
Theoretical weight: 3.9 KDa
Source organism: Acanthamoeba polyphaga mimivirus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand FMT 2 x FMT
1 modified residue:
Ligand OHU 2 x OHU

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 39.703Å b: 121.594Å c: 81.121Å
α: 90° β: 95.49° γ: 90°
R-values:
R R work R free
0.218 0.213 0.266
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Base excision repair: a critical player in many games.
Wallace SS. (2014)
7 more

4 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
3 more