› 7p9z

X-ray diffraction
1.33Å resolution

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

Released:
DOI: 10.2210/pdb7p9z/pdb
PDB entry 7p9z coloured by chain, front view.
PDB entry 7p9z coloured by chain, side view.
PDB entry 7p9z 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
OpenAccess logo 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-121778 (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
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)*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*AP*AP*AP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 9 nucleotides
Theoretical weight: 2.79 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: C2
Unit cell:
a: 61.848Å b: 68.775Å c: 68.424Å
α: 90° β: 90.35° γ: 90°
R-values:
R R work R free
0.175 0.174 0.186
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)