6G1C

Crystal structure of the N-terminal domain of Burkholderia Pseudomallei antitoxin HicB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6G1N


Literature

The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.

Winter, A.J.Williams, C.Isupov, M.N.Crocker, H.Gromova, M.Marsh, P.Wilkinson, O.J.Dillingham, M.S.Harmer, N.J.Titball, R.W.Crump, M.P.

(2018) J Biol Chem 293: 19429-19440

  • DOI: https://doi.org/10.1074/jbc.RA118.005173
  • Primary Citation of Related Structures:  
    6G1C, 6G1N, 6G26

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of hicAB in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.


  • Organizational Affiliation

    From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin HicBA [auth V],
B [auth A],
C [auth B],
D [auth C]
92Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSS0391
UniProt
Find proteins for Q63NA5 (Burkholderia pseudomallei (strain K96243))
Explore Q63NA5 
Go to UniProtKB:  Q63NA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63NA5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.447α = 90
b = 76.685β = 90
c = 76.907γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J014400/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Structure summary