X-ray diffraction
1.7Å resolution

Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing cytosine opposite to lesion)

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 trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
N-glycosylase/DNA lyase Chain: A
Molecule details ›
Chain: A
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') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.56 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*AP*AP*AP*CP*AP*AP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 9 nucleotides
Theoretical weight: 2.77 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
Spacegroup: C2221
Unit cell:
a: 59.599Å b: 71.832Å c: 138.535Å
α: 90° β: 90° γ: 90°
R R work R free
0.168 0.166 0.206
Expression systems:
  • Escherichia coli
  • Not provided