4YG4

HipB-O1-O1* complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.267 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

HipBA-promoter structures reveal the basis of heritable multidrug tolerance.

Schumacher, M.A.Balani, P.Min, J.Chinnam, N.B.Hansen, S.Vulic, M.Lewis, K.Brennan, R.G.

(2015) Nature 524: 59-64

  • DOI: https://doi.org/10.1038/nature14662
  • Primary Citation of Related Structures:  
    4YG1, 4YG4, 4YG7, 5K98

  • PubMed Abstract: 

    Multidrug tolerance is largely responsible for chronic infections and caused by a small population of dormant cells called persisters. Selection for survival in the presence of antibiotics produced the first genetic link to multidrug tolerance: a mutant in the Escherichia coli hipA locus. HipA encodes a serine-protein kinase, the multidrug tolerance activity of which is neutralized by binding to the transcriptional regulator HipB and hipBA promoter. The physiological role of HipA in multidrug tolerance, however, has been unclear. Here we show that wild-type HipA contributes to persister formation and that high-persister hipA mutants cause multidrug tolerance in urinary tract infections. Perplexingly, high-persister mutations map to the N-subdomain-1 of HipA far from its active site. Structures of higher-order HipA-HipB-promoter complexes reveal HipA forms dimers in these assemblies via N-subdomain-1 interactions that occlude their active sites. High-persistence mutations, therefore, diminish HipA-HipA dimerization, thereby unleashing HipA to effect multidrug tolerance. Thus, our studies reveal the mechanistic basis of heritable, clinically relevant antibiotic tolerance.


  • Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin HipBA,
B,
E [auth C],
F [auth D]
71Escherichia coli K-12Mutation(s): 0 
Gene Names: hipBb1508JW1501
UniProt
Find proteins for P23873 (Escherichia coli (strain K12))
Explore P23873 
Go to UniProtKB:  P23873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23873
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (28-MER)C [auth T]28Escherichia coli
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*A)-3')D [auth F]20Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.65α = 90
b = 69.8β = 93.1
c = 78.3γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description