› 4pcz

X-ray diffraction
1.7Å resolution

Crystal structure of a complex between R247G LlFPG mutant and a THF containing DNA

Released:
DOI: 10.2210/pdb4pcz/pdb
PDB 4pcz coloured by chain and viewed from the front.
PDB 4pcz coloured by chain and viewed from the side.
PDB 4pcz coloured by chain and viewed from the top.
Source organisms:
Entry authors: Coste F, Castaing B

Function and Biology Details

Reactions catalysed: 
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
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Formamidopyrimidine-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 31.02 KDa
Source organism: Lactococcus cremoris
Expression system: Escherichia coli
UniProt:
  • Canonical: P42371 (Residues: 2-273; 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
Source organism: synthetic construct
Expression system: Not provided
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
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P41212
Unit cell:
a: 91.723Å b: 91.723Å c: 142.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.157 0.182
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets.
Hans et al. (2020)
2 more

2 mentions without citation

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