› 4pd2

X-ray diffraction
1.65Å resolution

Crystal structure of a complex between a C248GH LlFpg mutant and a THF containing DNA

Released:
DOI: 10.2210/pdb4pd2/pdb
PDB entry 4pd2 coloured by chain, front view.
PDB entry 4pd2 coloured by chain, side view.
PDB entry 4pd2 coloured by chain, top view.
Source organism: Lactococcus cremoris
Primary publication:
Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Cieśla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B
Nucleic Acids Res 42 10748-61 (2014)
PMID: 25143530

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-117967 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Formamidopyrimidine-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 272 amino acids
Theoretical weight: 31.21 KDa
Source organism: Lactococcus cremoris
Expression system: Escherichia coli
UniProt:
  • Canonical: P42371 (Residues: 2-249, 250-273; Coverage: 99%)
Gene names: fpg, mutM
Sequence domains:
Structure domains:
DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.05 KDa
DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.36 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P41212
Unit cell:
a: 91.456Å b: 91.456Å c: 140.389Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.152 0.179
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases.
Boiteux et al. (2017)
2 more

1 mention without citation

Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Biela et al. (2014)