X-ray diffraction
2.04Å resolution

Crystal structure of a trapped Pab-AGOG/single-standed DNA covalent intermediate

Entry authors: Coste F, Goffinont S, Flament D, Castaing B

Function and Biology Details

Reaction 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
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
N-glycosylase/DNA lyase Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 242 amino acids
Theoretical weight: 27.98 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
  • Canonical: Q9UZY0 (Residues: 1-239; Coverage: 100%)
Gene names: PAB1695, PYRAB10170
Sequence domains: N-glycosylase/DNA lyase
DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3') Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 9 nucleotides
Theoretical weight: 2.56 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
Spacegroup: P1
Unit cell:
a: 39.743Å b: 74.259Å c: 101.726Å
α: 92.48° β: 100.74° γ: 105.46°
R R work R free
0.178 0.175 0.223
Expression systems:
  • Escherichia coli
  • Not provided