› 7p0w

X-ray diffraction
1.12Å resolution

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

Released:
DOI: 10.2210/pdb7p0w/pdb
PDB entry 7p0w coloured by chain, front view.
PDB entry 7p0w coloured by chain, side view.
PDB entry 7p0w coloured by chain, top view.
Source organisms:
Primary publication:
Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Franck C, Stéphane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C
Nucleic Acids Res 50 11072-11092 (2022)
PMID: 36300625

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
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121770 (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
UniProt:
  • 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*TP*AP*AP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 9 nucleotides
Theoretical weight: 2.78 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MPD 2 x MPD
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2221
Unit cell:
a: 59.776Å b: 71.578Å c: 138.691Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.125 0.124 0.143
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold.
Caffrey et al. (2023)

1 mention without citation

Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Franck et al. (2022)