› 2ibk

X-ray diffraction
2.25Å resolution

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Released:
DOI: 10.2210/pdb2ibk/pdb
PDB entry 2ibk coloured by chain, front view.
PDB entry 2ibk coloured by chain, side view.
PDB entry 2ibk coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.
Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H
Proc Natl Acad Sci U S A 104 14905-10 (2007)
PMID: 17848527

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-115390 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
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*AP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.42 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chain: E
Molecule details ›
Chain: E
Length: 17 nucleotides
Theoretical weight: 5.06 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand BAP 1 x BAP
Ligand EDO 3 x EDO
Ligand GOL 1 x GOL
Ligand CA 2 x CA
Ligand POP 1 x POP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21212
Unit cell:
a: 96.714Å b: 100.473Å c: 52.332Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.25 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

Y-family DNA polymerases and their role in tolerance of cellular DNA damage.
Sale et al. (2012)
10 more

3 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
2 more