› 3zf5

X-ray diffraction
3.2Å resolution

Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y84F mutant with dUpNHpp).

Released:
DOI: 10.2210/pdb3zf5/pdb
PDB entry 3zf5 coloured by chain, front view.
PDB entry 3zf5 coloured by chain, side view.
PDB entry 3zf5 coloured by chain, top view.
Source organism: Staphylococcus virus 80alpha
Primary publication:
Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism.
Tormo-Más MÁ, Donderis J, García-Caballer M, Alt A, Mir-Sanchis I, Marina A, Penadés JR
Mol Cell 49 947-58 (2013)
PMID: 23333307

Function and Biology Details

Reaction catalysed: 
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107512 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dUTP diphosphatase Chain: A
Molecule details ›
Chain: A
Length: 204 amino acids
Theoretical weight: 22.65 KDa
Source organism: Staphylococcus virus 80alpha
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A4ZF98 (Residues: 1-170; Coverage: 100%)
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

3 bound ligands:
Ligand DUP 1 x DUP
Ligand NI 2 x NI
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P213
Unit cell:
a: 88.24Å b: 88.24Å c: 88.24Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.222 0.277
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites.
Penadés et al. (2015)
2 more