Shewanella oneidensis Toxin Antitoxin System Toxin Protein HipA Bound with AMPPNP and Mg

Experimental Data Snapshot

  • Resolution: 1.83 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence.

Wen, Y.Behiels, E.Felix, J.Elegheert, J.Vergauwen, B.Devreese, B.Savvides, S.N.

(2014) Nucleic Acids Res 42: 10134-10147

  • DOI: https://doi.org/10.1093/nar/gku665
  • Primary Citation of Related Structures:  
    4PU3, 4PU4, 4PU5, 4PU7, 4PU8

  • PubMed Abstract: 

    Nearly all bacteria exhibit a type of phenotypic growth described as persistence that is thought to underlie antibiotic tolerance and recalcitrant chronic infections. The chromosomally encoded high-persistence (Hip) toxin-antitoxin proteins HipASO and HipBSO from Shewanella oneidensis, a proteobacterium with unusual respiratory capacities, constitute a type II toxin-antitoxin protein module. Here we show that phosphorylated HipASO can engage in an unexpected ternary complex with HipBSO and double-stranded operator DNA that is distinct from the prototypical counterpart complex from Escherichia coli. The structure of HipBSO in complex with operator DNA reveals a flexible C-terminus that is sequestered by HipASO in the ternary complex, indicative of its role in binding HipASO to abolish its function in persistence. The structure of HipASO in complex with a non-hydrolyzable ATP analogue shows that HipASO autophosphorylation is coupled to an unusual conformational change of its phosphorylation loop. However, HipASO is unable to phosphorylate the translation factor Elongation factor Tu, contrary to previous reports, but in agreement with more recent findings. Our studies suggest that the phosphorylation state of HipA is an important factor in persistence and that the structural and mechanistic diversity of HipAB modules as regulatory factors in bacterial persistence is broader than previously thought.

  • Organizational Affiliation

    Unit for Biological Mass Spectrometry and Proteomics, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium bart.devreese@ugent.be.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin-antitoxin system toxin HipA family453Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_0706hipA
Find proteins for Q8EIX3 (Shewanella oneidensis (strain MR-1))
Explore Q8EIX3 
Go to UniProtKB:  Q8EIX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EIX3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.83 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.7α = 90
b = 75.83β = 90
c = 110.32γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-09-17
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description