5CZE

Crystal structure of the PaaA2-ParE2 antitoxin-toxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PaaA2A,
C,
E [auth I],
G [auth K]
71Escherichia coli O157:H7 str. SS52Mutation(s): 0 
Gene Names: SS52_2228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmid stabilization protein ParEB,
D,
F [auth J],
H [auth L]
100Escherichia coli O157:H7 str. SS52Mutation(s): 0 
Gene Names: relE2AML07_29260APZ14_24120ARC77_01680ERS085383_05243ERS085404_05085ERS150873_04952JEONG1266_09605
UniProt
Find proteins for A0A0D7C2L1 (Escherichia coli)
Explore A0A0D7C2L1 
Go to UniProtKB:  A0A0D7C2L1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D7C2L1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C,
E [auth I],
G [auth K]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.226α = 90
b = 143.226β = 90
c = 86.63γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description