3ZF1

Phage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase D81N mutant with dUpNHpp).

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.molcel.2012.12.013
  • Primary Citation of Related Structures:  

  • 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 mod ...

    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.

    Related Citations: 
    • Moonlighting Bacteriophage Proteins Derepress Staphylococcal Pathogenicity Islands.
      Tormo-Mas, M.A.,Mir, I.,Shrestha, A.,Tallent, S.M.,Campoy, S.,Lasa, I.,Barbe, J.,Novick, R.P.,Christie, G.E.,Penades, J.R.
      (2010) Nature 465: 779

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUTPASE
A
204Staphylococcus virus 80alphaMutations: N115D
Find proteins for A4ZF98 (Staphylococcus virus 80alpha)
Go to UniProtKB:  A4ZF98
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP
Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.230 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 87.210α = 90.00
b = 87.210β = 90.00
c = 87.210γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Database references
  • Version 1.2: 2013-04-03
    Type: Other, Refinement description, Structure summary
  • Version 1.3: 2013-04-17
    Type: Database references, Other, Structure summary