› 3khl

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb3khl/pdb
PDB entry 3khl coloured by chain, front view.
PDB entry 3khl coloured by chain, side view.
PDB entry 3khl 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-116480 (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(*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*AP*(DDG))-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(*CP*C*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: 20 nucleotides
Theoretical weight: 5.97 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand TTP 2 x TTP
Ligand CA 6 x CA
Ligand AF 2 x AF
1 modified residue:
Ligand DDG 2 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 52.389Å b: 52.674Å c: 100.103Å
α: 82.19° β: 76.4° γ: 70.07°
R-values:
R R work R free
0.208 0.205 0.263
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

3 mentions without citation

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