› 2c28

X-ray diffraction
2.27Å resolution

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

Released:
DOI: 10.2210/pdb2c28/pdb
PDB entry 2c28 coloured by chain, front view.
PDB entry 2c28 coloured by chain, side view.
PDB entry 2c28 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.
Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP
J Biol Chem 281 2358-72 (2006)
PMID: 16306039

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-506785 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 41.09 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*C)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.39 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DG 1 x DG
Ligand CA 3 x CA
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P21212
Unit cell:
a: 93.355Å b: 102.03Å c: 52.826Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.239 0.256
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

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