3DD9

Structure of DocH66Y dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The intrinsically disordered domain of the antitoxin Phd chaperones the toxin Doc against irreversible inactivation and misfolding

De Gieter, S.Konijnenberg, A.Talavera, A.Butterer, A.Haesaerts, S.De Greve, H.Sobott, F.Loris, R.Garcia-Pino, A.

(2014) J. Biol. Chem. 289: 34013-34023

  • DOI: 10.1074/jbc.M114.572396

  • PubMed Abstract: 
  • The toxin Doc from the phd/doc toxin-antitoxin module targets the cellular translation machinery and is inhibited by its antitoxin partner Phd. Here we show that Phd also functions as a chaperone, keeping Doc in an active, correctly folded conformati ...

    The toxin Doc from the phd/doc toxin-antitoxin module targets the cellular translation machinery and is inhibited by its antitoxin partner Phd. Here we show that Phd also functions as a chaperone, keeping Doc in an active, correctly folded conformation. In the absence of Phd, Doc exists in a relatively expanded state that is prone to dimerization through domain swapping with its active site loop acting as hinge region. The domain-swapped dimer is not capable of arresting protein synthesis in vitro, whereas the Doc monomer is. Upon binding to Phd, Doc becomes more compact and is secured in its monomeric state with a neutralized active site.


    Organizational Affiliation

    From Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Molecular Recognition Unit (MoRe).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death on curing protein
A, B, C, D, E, F, G, H
135Escherichia phage P1Mutation(s): 2 
Gene Names: doc
EC: 2.7.11.1
Find proteins for Q06259 (Escherichia phage P1)
Go to UniProtKB:  Q06259
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.084α = 90.00
b = 197.988β = 93.04
c = 54.109γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-07-23
    Type: Other
  • Version 1.3: 2018-03-07
    Type: Database references