6OTT

Structure of PurF in complex with ppApp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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This is version 1.3 of the entry. See complete history


Literature

An interbacterial toxin inhibits target cell growth by synthesizing (p)ppApp.

Ahmad, S.Wang, B.Walker, M.D.Tran, H.R.Stogios, P.J.Savchenko, A.Grant, R.A.McArthur, A.G.Laub, M.T.Whitney, J.C.

(2019) Nature 575: 674-678

  • DOI: https://doi.org/10.1038/s41586-019-1735-9
  • Primary Citation of Related Structures:  
    6OTT, 6OX6

  • PubMed Abstract: 

    Bacteria have evolved sophisticated mechanisms to inhibit the growth of competitors 1 . One such mechanism involves type VI secretion systems, which bacteria can use to inject antibacterial toxins directly into neighbouring cells. Many of these toxins target the integrity of the cell envelope, but the full range of growth inhibitory mechanisms remains unknown 2 . Here we identify a type VI secretion effector, Tas1, in the opportunistic pathogen Pseudomonas aeruginosa. The crystal structure of Tas1 shows that it is similar to enzymes that synthesize (p)ppGpp, a broadly conserved signalling molecule in bacteria that modulates cell growth rate, particularly in response to nutritional stress 3 . However, Tas1 does not synthesize (p)ppGpp; instead, it pyrophosphorylates adenosine nucleotides to produce (p)ppApp at rates of nearly 180,000 molecules per minute. Consequently, the delivery of Tas1 into competitor cells drives rapid accumulation of (p)ppApp, depletion of ATP, and widespread dysregulation of essential metabolic pathways, thereby resulting in target cell death. Our findings reveal a previously undescribed mechanism for interbacterial antagonism and demonstrate a physiological role for the metabolite (p)ppApp in bacteria.


  • Organizational Affiliation

    Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidophosphoribosyltransferase, PurF
A, B
504Escherichia coli K-12Mutation(s): 0 
Gene Names: purFb2312JW2309
EC: 2.4.2.14
UniProt
Find proteins for P0AG16 (Escherichia coli (strain K12))
Explore P0AG16 
Go to UniProtKB:  P0AG16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG16
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.23α = 90
b = 156.83β = 90
c = 107.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesR01GM08289
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2019-12-11
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations