› 3khg

X-ray diffraction
2.96Å resolution

Dpo4 extension ternary complex with misinserted A opposite the 2-aminofluorene-guanine [AF]G lesion

Released:
DOI: 10.2210/pdb3khg/pdb
PDB entry 3khg coloured by chain, front view.
PDB entry 3khg coloured by chain, side view.
PDB entry 3khg coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ
Nat Struct Mol Biol 17 379-88 (2010)
PMID: 20154704

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-116478 (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: 38.95 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 2-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' Chains: D, H
Molecule details ›
Chains: D, H
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' Chains: E, J
Molecule details ›
Chains: E, J
Length: 19 nucleotides
Theoretical weight: 5.68 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand DGT 2 x DGT
Ligand CA 6 x CA
Ligand EPE 1 x EPE
Ligand AF 2 x AF
1 modified residue:
Ligand 2DA 2 x 2DA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 52.811Å b: 110.948Å c: 100.772Å
α: 90° β: 101.38° γ: 90°
R-values:
R R work R free
0.209 0.205 0.282
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Lethal mutagenesis: targeting the mutator phenotype in cancer.
Fox et al. (2010)
1 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