4ZM2

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.88 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.

Garcia-Pino, A.De Gieter, S.Talavera, A.De Greve, H.Efremov, R.G.Loris, R.

(2016) Nat Chem Biol 12: 490-496

  • DOI: 10.1038/nchembio.2078
  • Primary Citation of Related Structures:  
    4ZLX, 4ZM0, 4ZM2

  • PubMed Abstract: 
  • Conditional cooperativity is a common mechanism involved in transcriptional regulation of prokaryotic type II toxin-antitoxin operons and is intricately related to bacterial persistence. It allows the toxin component of a toxin-antitoxin module to act as a co-repressor at low doses of toxin as compared to antitoxin ...

    Conditional cooperativity is a common mechanism involved in transcriptional regulation of prokaryotic type II toxin-antitoxin operons and is intricately related to bacterial persistence. It allows the toxin component of a toxin-antitoxin module to act as a co-repressor at low doses of toxin as compared to antitoxin. When toxin level exceeds a certain threshold, however, the toxin becomes a de-repressor. Most antitoxins contain an intrinsically disordered region (IDR) that typically is involved in toxin neutralization and repressor complex formation. To address how the antitoxin IDR is involved in transcription regulation, we studied the phd-doc operon from bacteriophage P1. We provide evidence that the IDR of Phd provides an entropic barrier precluding full operon repression in the absence of Doc. Binding of Doc results in a cooperativity switch and consequent strong operon repression, enabling context-specific modulation of the regulatory process. Variations of this theme are likely to be a common mechanism in the autoregulation of bacterial operons that involve intrinsically disordered regions.


    Organizational Affiliation

    Structural Biology Research Center, VIB, Brussels, Belgium.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antitoxin phdA, B, C, D73Escherichia virus P1Mutation(s): 0 
Gene Names: phd
UniProt
Find proteins for Q06253 (Escherichia phage P1)
Explore Q06253 
Go to UniProtKB:  Q06253
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')E, G14Escherichia virus P1
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')F, H14Escherichia virus P1
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.88 Å
      • R-Value Free: 0.271 
      • R-Value Work: 0.262 
      • R-Value Observed: 0.262 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 65.87α = 90
      b = 56.58β = 111.47
      c = 74.84γ = 90
      Software Package:
      Software NamePurpose
      BUSTERrefinement
      XDSdata reduction
      XDSdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2016-04-20
        Type: Initial release
      • Version 1.1: 2016-05-04
        Changes: Database references
      • Version 1.2: 2016-05-18
        Changes: Database references
      • Version 1.3: 2016-06-29
        Changes: Database references