4PU3

Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex (space group P212121)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1093/nar/gku665
  • Primary Citation of Related Structures:  

  • 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 an ...

    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 Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxin-antitoxin system toxin HipA family
A, B
454Shewanella oneidensis (strain MR-1)Mutation(s): 0 
Gene Names: hipA
EC: 2.7.11.1
Find proteins for Q8EIX3 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8EIX3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Toxin-antitoxin system antidote transcriptional repressor Xre family
D, C
118Shewanella oneidensis (strain MR-1)Mutation(s): 0 
Gene Names: hipB
Find proteins for Q8EIX4 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8EIX4
Entity ID: 3
MoleculeChainsLengthOrganism
Operator DNAQ26Shewanella oneidensis
Entity ID: 4
MoleculeChainsLengthOrganism
Operator DNAP26Shewanella oneidensis
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.820α = 90.00
b = 122.450β = 90.00
c = 189.850γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
AMoREphasing
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Database references