PDBe 1nnj

X-ray diffraction
1.9Å resolution

Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing 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 Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 31.08 KDa
Source organism: Lactococcus lactis
Expression system: Escherichia coli
UniProt:
  • Canonical: P42371 (Residues: 2-273; Coverage: 99%)
Gene names: fpg, mutM
Sequence domains: Zinc finger found in FPG and IleRS
Structure domains:
5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3' Chain: E
Molecule details ›
Chain: E
Length: 14 nucleotides
Theoretical weight: 4.36 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.01 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P41212
Unit cell:
a: 92.15Å b: 92.15Å c: 142.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.236
Expression systems:
  • Escherichia coli
  • Not provided