3ZF0

Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase D81A mutant with dUpNHpp).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Phage Dutpases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-Like Mechanism.

Tormo-Mas, M.A.Donderis, J.Garcia-Caballer, M.Alt, A.Mir-Sanchis, I.Marina, A.Penades, J.R.

(2013) Mol Cell 49: 947

  • DOI: https://doi.org/10.1016/j.molcel.2012.12.013
  • Primary Citation of Related Structures:  
    3ZEZ, 3ZF0, 3ZF1, 3ZF2, 3ZF3, 3ZF4, 3ZF5, 3ZF6

  • PubMed Abstract: 

    dUTPases (Duts) have emerged as promising regulatory molecules controlling relevant cellular processes. However, the mechanism underlying this regulatory function remains enigmatic. Using staphylococcal pathogenicity island (SaPI) repression as a model, we report here that phage Duts induce the transfer of SaPI-encoded virulence factors by switching between active (dUTP-bound) and inactive (apo state) conformations, a conversion catalyzed by their intrinsic dUTPase activity. Crystallographic and mutagenic analyses demonstrate that binding to dUTP reorders the C-terminal motif V of the phage-encoded Duts, rendering these proteins into the active conformation required for SaPI derepression. By contrast, the conversion to the apo state conformation by hydrolysis of the bound dUTP generates a protein that is unable to induce the SaPI cycle. Because none of the requirements involving Duts in SaPI transfer are exclusive to the phage-encoded proteins, we propose that Duts are widespread cellular regulators acting in a manner analogous to the eukaryotic G proteins.


  • Organizational Affiliation

    Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA), Segorbe, 12400 Castellón, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUTPASE204Dubowvirus dv80alphaMutation(s): 1 
EC: 3.6.1.23
UniProt
Find proteins for A4ZF98 (Staphylococcus phage 80alpha)
Explore A4ZF98 
Go to UniProtKB:  A4ZF98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZF98
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.12α = 90
b = 87.12β = 90
c = 87.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references
  • Version 1.2: 2013-04-03
    Changes: Other, Structure summary
  • Version 1.3: 2013-04-17
    Changes: Database references, Other, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other