› 2ago

X-ray diffraction
2.85Å resolution

Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis

Released:
DOI: 10.2210/pdb2ago/pdb
PDB entry 2ago coloured by chain, front view.
PDB entry 2ago coloured by chain, side view.
PDB entry 2ago coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.
Vaisman A, Ling H, Woodgate R, Yang W
EMBO J 24 2957-67 (2005)
PMID: 16107880

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-506742 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 39.02 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(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.43 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.06 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand CA 1 x CA
Ligand POP 1 x POP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 99.044Å b: 101.939Å c: 53.017Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.263
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Yang et al. (2006)
10 more

4 mentions without citation

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