› 2r8h

X-ray diffraction
2.48Å resolution

Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2-Propanodeoxyguanosine (PdG) by the Sulfolobus solfataricus DNA Polymerase Dpo4 Polymerase

Released:
DOI: 10.2210/pdb2r8h/pdb
PDB entry 2r8h coloured by chain, front view.
PDB entry 2r8h coloured by chain, side view.
PDB entry 2r8h coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV.
Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP
Biochemistry 47 7322-34 (2008)
PMID: 18563918

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-115825 (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
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DC)-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
DNA (5'-D(*DTP*DCP*DAP*DCP*(P)P*DGP*DAP*DAP*DTP*DCP*DCP*DTP*DTP*DCP*DCP*DCP*DCP*DC)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.41 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand DGT 1 x DGT
1 modified residue:
Ligand P 1 x P

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21212
Unit cell:
a: 93.4Å b: 103Å c: 52.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.279
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Chemistry and biology of DNA containing 1,N(2)-deoxyguanosine adducts of the alpha,beta-unsaturated aldehydes acrolein, crotonaldehyde, and 4-hydroxynonenal.
Minko et al. (2009)
4 more

3 mentions without citation

Homology modelling and spectroscopy, a never-ending love story.
Venselaar et al. (2010)
2 more