› 1n56

X-ray diffraction
2.4Å resolution

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion

Released:
DOI: 10.2210/pdb1n56/pdb
PDB entry 1n56 coloured by chain, front view.
PDB entry 1n56 coloured by chain, side view.
PDB entry 1n56 coloured by chain, top view.
Source organisms:
Primary publication:
Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.
Ling H, Boudsocq F, Woodgate R, Yang W
Mol Cell 13 751-62 (2004)
PMID: 15023344

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-114232 (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: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus
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*CP*TP*AP*A)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 14 nucleotides
Theoretical weight: 4.42 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 17 nucleotides
Theoretical weight: 4.93 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand ATP 2 x ATP
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200HB
Spacegroup: P212121
Unit cell:
a: 98.016Å b: 102.358Å c: 105.66Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.225 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

20 review citations

Y-family DNA polymerases and their role in tolerance of cellular DNA damage.
Sale et al. (2012)
19 more

2 mentions without citation

RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa.
Gening et al. (2006)
1 more