PDBe 1kfv

X-ray diffraction
2.55Å resolution

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP 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. 
Biochemical function:
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
Molecule details ›
Chains: A, B
Length: 271 amino acids
Theoretical weight: 31.26 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*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3' Chains: E, H
Molecule details ›
Chains: E, H
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3' Chains: D, G
Molecule details ›
Chains: D, G
Length: 13 nucleotides
Theoretical weight: 3.68 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21
Unit cell:
a: 69.88Å b: 62.03Å c: 80.97Å
α: 90° β: 104.7° γ: 90°
R-values:
R R work R free
0.251 0.251 0.285
Expression systems:
  • Escherichia coli
  • Not provided