PDBe 1k82

X-ray diffraction
2.1Å resolution

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

Released:

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. 
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Formamidopyrimidine-DNA glycosylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 268 amino acids
Theoretical weight: 30.2 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P05523 (Residues: 2-269; Coverage: 100%)
Gene names: JW3610, b3635, fpg, mutM
Sequence domains:
Structure domains:
5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3' Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 13 nucleotides
Theoretical weight: 3.86 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P21
Unit cell:
a: 80.704Å b: 96.033Å c: 96.228Å
α: 90° β: 96.799° γ: 90°
R-values:
R R work R free
0.214 0.214 0.265
Expression systems:
  • Escherichia coli
  • Not provided