3K33

Crystal structure of the Phd-Doc complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity.

Garcia-Pino, A.Balasubramanian, S.Wyns, L.Gazit, E.De Greve, H.Magnuson, R.D.Charlier, D.van Nuland, N.A.Loris, R.

(2010) Cell 142: 101-111

  • DOI: 10.1016/j.cell.2010.05.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regulation of the phd/doc toxin-antitoxin operon involves the toxin Doc as co- or derepressor depending on the ratio between Phd and Doc, a phenomenon known as conditional cooperativity. The mechanism underlying this observed behavior is not understo ...

    Regulation of the phd/doc toxin-antitoxin operon involves the toxin Doc as co- or derepressor depending on the ratio between Phd and Doc, a phenomenon known as conditional cooperativity. The mechanism underlying this observed behavior is not understood. Here we show that monomeric Doc engages two Phd dimers on two unrelated binding sites. The binding of Doc to the intrinsically disordered C-terminal domain of Phd structures its N-terminal DNA-binding domain, illustrating allosteric coupling between highly disordered and highly unstable domains. This allosteric effect also couples Doc neutralization to the conditional regulation of transcription. In this way, higher levels of Doc tighten repression up to a point where the accumulation of toxin triggers the production of Phd to counteract its action. Our experiments provide the basis for understanding the mechanism of conditional cooperative regulation of transcription typical of toxin-antitoxin modules. This model may be applicable for the regulation of other biological systems.


    Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussels, Pleinlaan 2, B-1050 Brussels, Belgium. agarciap@vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death on curing protein
A
126Escherichia phage P1Mutation(s): 0 
Gene Names: doc
EC: 2.7.11.1
Find proteins for Q06259 (Escherichia phage P1)
Go to UniProtKB:  Q06259
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prevent host death protein
B, C, D
73Escherichia phage P1Mutation(s): 0 
Gene Names: phd
Find proteins for Q06253 (Escherichia phage P1)
Go to UniProtKB:  Q06253
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polypeptide of unknown amino acids and source
E
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
E
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.295α = 90.00
b = 48.295β = 90.00
c = 347.321γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
MAR345dtbdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance