› 4yig

X-ray diffraction
2.7Å resolution

vaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free uracyl

Released:
DOI: 10.2210/pdb4yig/pdb
PDB entry 4yig coloured by chain, front view.
PDB entry 4yig coloured by chain, side view.
PDB entry 4yig coloured by chain, top view.
Source organism: Vaccinia virus Copenhagen
Primary publication:
Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.
Burmeister WP, Tarbouriech N, Fender P, Contesto-Richefeu C, Peyrefitte CN, Iseni F
J Biol Chem 290 17923-17934 (2015)
PMID: 26045555

Function and Biology Details

Reaction catalysed: 
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118319 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Uracil-DNA glycosylase Chains: A, E, I
Molecule details ›
Chains: A, E, I
Length: 232 amino acids
Theoretical weight: 26.73 KDa
Source organism: Vaccinia virus Copenhagen
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20536 (Residues: 1-218; Coverage: 100%)
Gene names: D4R, OPG116, UNG
Structure domains: Uracil-DNA glycosylase-like domain
DNA polymerase processivity factor component OPG148 Chains: B, F, J
Molecule details ›
Chains: B, F, J
Length: 52 amino acids
Theoretical weight: 5.78 KDa
Source organism: Vaccinia virus Copenhagen
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20995 (Residues: 3-50; Coverage: 11%)
Gene names: A20R, OPG148
Structure domains: Helix Hairpins
DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3') Chains: C, G, K
Molecule details ›
Chains: C, G, K
Length: 10 nucleotides
Theoretical weight: 2.89 KDa
DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3') Chains: D, H, L
Molecule details ›
Chains: D, H, L
Length: 10 nucleotides
Theoretical weight: 3.09 KDa

Ligands and Environments

1 bound ligand:
Ligand URA 3 x URA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P65
Unit cell:
a: 136.092Å b: 136.092Å c: 161.073Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.18 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The French Armed Forces Virology Unit: A Chronological Record of Ongoing Research on Orthopoxvirus.
Delaune et al. (2017)
9 other articles

6 mentions without citation

The vaccinia virus DNA polymerase and its processivity factor.
Czarnecki et al. (2017)
5 more