› 3pvx

X-ray diffraction
3.03Å resolution

Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV

Released:
DOI: 10.2210/pdb3pvx/pdb
PDB entry 3pvx coloured by chain, front view.
PDB entry 3pvx coloured by chain, side view.
PDB entry 3pvx coloured by chain, top view.
Source organisms:
Primary publication:
Bypass of aflatoxin B1 adducts by the Sulfolobus solfataricus DNA polymerase IV.
Banerjee S, Brown KL, Egli M, Stone MP
J Am Chem Soc 133 12556-68 (2011)
PMID: 21790157

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116715 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 39.85 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*AP*TP*TP*(PVX)P*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 5.11 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 3 x CA
1 modified residue:
Ligand PVX 1 x PVX

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21212
Unit cell:
a: 94.752Å b: 103.905Å c: 52.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.299
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

The formamidopyrimidines: purine lesions formed in competition with 8-oxopurines from oxidative stress.
Greenberg MM. (2012)
2 more

1 mention without citation

Bypass of aflatoxin B1 adducts by the Sulfolobus solfataricus DNA polymerase IV.
Banerjee et al. (2011)