› 5myd

X-ray diffraction
2.3Å resolution

Convergent evolution involving dimeric and trimeric dUTPases in signalling.

Released:
DOI: 10.2210/pdb5myd/pdb
PDB entry 5myd coloured by chain, front view.
PDB entry 5myd coloured by chain, side view.
PDB entry 5myd coloured by chain, top view.
Source organism: Staphylococcus sp. HMSC068C09
Primary publication:
Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization.
Donderis J, Bowring J, Maiques E, Ciges-Tomas JR, Alite C, Mehmedov I, Tormo-Mas MA, Penadés JR, Marina A
PLoS Pathog 13 e1006581 (2017)
PMID: 28892519

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104155 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dUTPase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 207 amino acids
Theoretical weight: 24.16 KDa
Source organism: Staphylococcus sp. HMSC068C09
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: A0A2D0TC86 (Residues: 1-187; Coverage: 100%)
Gene name: HMPREF2930_08375
Sequence domains: dUTPase

Ligands and Environments

2 bound ligands:
Ligand DUP 4 x DUP
Ligand MG 8 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04, ALBA BEAMLINE XALOC
Spacegroup: P21
Unit cell:
a: 69.89Å b: 81.44Å c: 81.53Å
α: 90° β: 106.92° γ: 90°
R-values:
R R work R free
0.226 0.224 0.265
Expression system: Escherichia coli BL21

Quick links

Citations

2 review citations

Phage satellites and their emerging applications in biotechnology.
Ibarra-Chávez et al. (2021)
1 more

3 mentions without citation

Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer.
Bowring et al. (2017)
2 more