› 1s0m

X-ray diffraction
2.7Å resolution

Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a DNA polymerase

Released:
DOI: 10.2210/pdb1s0m/pdb
PDB entry 1s0m coloured by chain, front view.
PDB entry 1s0m coloured by chain, side view.
PDB entry 1s0m coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.
Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F, Woodgate R, Jerina DM, Yang W
Proc Natl Acad Sci U S A 101 2265-9 (2004)
PMID: 14982998

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-506502 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*T)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4.11 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(P*AP*TP*AP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*CP*A)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 16 nucleotides
Theoretical weight: 4.76 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand BAP 2 x BAP
Ligand CA 7 x CA
Ligand MG 1 x MG
Ligand DTP 2 x DTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 100.029Å b: 103.545Å c: 106.127Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.207 0.246
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance.
Waters et al. (2009)
10 more

13 mentions without citation

Translesion DNA polymerases.
Goodman et al. (2013)
12 more