4ZM0

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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
  • Structures With Same Primary Citation

  • 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 ac ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antitoxin phdA, B, C, D73Escherichia virus P1Mutation(s): 0 
Gene Names: phd
Find proteins for Q06253 (Escherichia phage P1)
Explore Q06253 
Go to UniProtKB:  Q06253
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')E, G14Escherichia virus P1
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*A)-3')F, H14Escherichia virus P1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
144
Query on 144

Download CCD File 
G
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.98α = 90
b = 165.98β = 90
c = 156.88γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Belgium--

Revision History 

  • 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