› 4jv0

X-ray diffraction
2.95Å resolution

Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4

Released:
DOI: 10.2210/pdb4jv0/pdb
PDB entry 4jv0 coloured by chain, front view.
PDB entry 4jv0 coloured by chain, side view.
PDB entry 4jv0 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4.
Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP
Chem Res Toxicol 26 1348-60 (2013)
PMID: 23947567

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117713 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 39.85 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(P*TP*(KAG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.39 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 1 x DTP
Ligand CA 2 x CA
1 modified residue:
Ligand KAG 1 x KAG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21212
Unit cell:
a: 93.826Å b: 104.486Å c: 52.529Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.192 0.27
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Recent insight into the kinetic mechanisms and conformational dynamics of Y-Family DNA polymerases.
Maxwell et al. (2014)
1 more

1 mention without citation

Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4.
Shanmugam et al. (2013)