6OX6

Crystal structure of the complex between the Type VI effector Tas1 and its immunity protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1038/s41586-019-1735-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteria have evolved sophisticated mechanisms to inhibit the growth of competitors <sup>1 </sup>. One such mechanism involves type VI secretion systems, which bacteria can use to inject antibacterial toxins directly into neighbouring cells. Many of ...

    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

    Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, Ontario, Canada.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada. jwhitney@mcmaster.ca.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada. jwhitney@mcmaster.ca.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada. jwhitney@mcmaster.ca.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tas1
A
439Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9I739 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I739
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PA14_01140
B
77Pseudomonas aeruginosaMutation(s): 0 
Find proteins for A0A090A233 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A090A233
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.631α = 90.00
b = 66.631β = 90.00
c = 148.307γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement
PHENIXrefinement
Cootmodel building
PHENIXmodel building
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Database references
  • Version 1.2: 2019-11-20
    Type: Database references
  • Version 1.3: 2019-12-11
    Type: Database references
  • Version 1.4: 2019-12-18
    Type: Author supporting evidence