› 2agp

X-ray diffraction
2.9Å resolution

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

Released:
DOI: 10.2210/pdb2agp/pdb
PDB entry 2agp coloured by chain, front view.
PDB entry 2agp coloured by chain, side view.
PDB entry 2agp 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-115071 (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: 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*(DOC)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4.08 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') Chains: D, F
Molecule details ›
Chains: D, F
Length: 17 nucleotides
Theoretical weight: 5.06 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 2 x CA
Ligand MG 5 x MG
Ligand DGT 2 x DGT
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 97.867Å b: 101.463Å c: 105.642Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.207 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

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

4 mentions without citation

Structural and Molecular Kinetic Features of Activities of DNA Polymerases.
Kuznetsova et al. (2022)
3 more