› 4f4x

X-ray diffraction
2.05Å resolution

Y-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #2

Released:
DOI: 10.2210/pdb4f4x/pdb
PDB entry 4f4x coloured by chain, front view.
PDB entry 4f4x coloured by chain, side view.
PDB entry 4f4x coloured by chain, top view.
Source organisms:
Primary publication:
Y-family polymerase conformation is a major determinant of fidelity and translesion specificity.
Wilson RC, Jackson MA, Pata JD
Structure 21 20-31 (2013)
PMID: 23245850

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117456 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 361 amino acids
Theoretical weight: 41.12 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-3, 231-352; Coverage: 36%)
  • Canonical: Q4JB80 (Residues: 4-231; Coverage: 64%)
Gene names: SSO2448, Saci_0554, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.32 KDa
DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 19 nucleotides
Theoretical weight: 5.76 KDa

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand DCP 1 x DCP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 101.122Å b: 102.306Å c: 52.879Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.218 0.25
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Translesion DNA polymerases in eukaryotes: what makes them tick?
Vaisman et al. (2017)
6 more

2 mentions without citation

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