5CZF

Crystal structure of the PaaA2-ParE2 antitoxin-toxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

A unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.

Sterckx, Y.G.Jove, T.Shkumatov, A.V.Garcia-Pino, A.Geerts, L.De Kerpel, M.Lah, J.De Greve, H.Van Melderen, L.Loris, R.

(2016) J Mol Biol 428: 1589-1603

  • DOI: https://doi.org/10.1016/j.jmb.2016.03.007
  • Primary Citation of Related Structures:  
    5CW7, 5CZE, 5CZF

  • PubMed Abstract: 

    Many bacterial pathogens modulate their metabolic activity, virulence and pathogenicity through so-called "toxin-antitoxin" (TA) modules. The genome of the human pathogen Escherichia coli O157 contains two three-component TA modules related to the known parDE module. Here, we show that the toxin EcParE2 maps in a branch of the RelE/ParE toxin superfamily that is distinct from the branches that contain verified gyrase and ribosome inhibitors. The structure of EcParE2 closely resembles that of Caulobacter crescentus ParE but shows a distinct pattern of conserved surface residues, in agreement with its apparent inability to interact with GyrA. The antitoxin EcPaaA2 is characterized by two α-helices (H1 and H2) that serve as molecular recognition elements to wrap itself around EcParE2. Both EcPaaA2 H1 and H2 are required to sustain a high-affinity interaction with EcParE2 and for the inhibition of EcParE2-mediated killing in vivo. Furthermore, evidence demonstrates that EcPaaA2 H2, but not H1, determines specificity for EcParE2. The initially formed EcPaaA2-EcParE2 heterodimer then assembles into a hetero-hexadecamer, which is stable in solution and is formed in a highly cooperative manner. Together these findings provide novel data on quaternary structure, TA interactions and activity of a hitherto poorly characterized family of TA modules.


  • Organizational Affiliation

    Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium; Structural Biology Research Centre, VIB, Pleinlaan 2, B-1050 Brussel, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PaaA2
A, B
52Escherichia coli O157Mutation(s): 0 
Gene Names: SS52_2228
UniProt
Find proteins for Q8XAD5 (Escherichia coli O157:H7)
Explore Q8XAD5 
Go to UniProtKB:  Q8XAD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XAD5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmid stabilization protein ParE
C, D
111Escherichia coli O157Mutation(s): 0 
Gene Names: relE2
UniProt
Find proteins for A0A0H3JHG3 (Escherichia coli O157:H7)
Explore A0A0H3JHG3 
Go to UniProtKB:  A0A0H3JHG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JHG3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.56α = 90
b = 91.56β = 90
c = 185.6γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description