› 4f4y

X-ray diffraction
2.34Å resolution

Y-family DNA polymerase chimera Dbh-Dpo4-Dbh

Released:
DOI: 10.2210/pdb4f4y/pdb
PDB entry 4f4y coloured by chain, front view.
PDB entry 4f4y coloured by chain, side view.
PDB entry 4f4y 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-117457 (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: 362 amino acids
Theoretical weight: 41.09 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-3, 231-247; Coverage: 6%)
  • Canonical: Q4JB80 (Residues: 4-231, 249-354; Coverage: 94%)
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*CP*CP*C)-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 19 nucleotides
Theoretical weight: 5.76 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 53.076Å b: 103.39Å c: 112.988Å
α: 90° β: 101.76° γ: 90°
R-values:
R R work R free
0.223 0.222 0.259
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

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