3KXE

A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Conserved Mode of Protein Recognition and Binding in a ParD-ParE Toxin-Antitoxin Complex.

Dalton, K.M.Crosson, S.

(2010) Biochemistry 49: 2205-2215

  • DOI: 10.1021/bi902133s

  • PubMed Abstract: 
  • Toxin-antitoxin (TA) systems form a ubiquitous class of prokaryotic proteins with functional roles in plasmid inheritance, environmental stress response, and cell development. ParDE family TA systems are broadly conserved on plasmids and bacterial ch ...

    Toxin-antitoxin (TA) systems form a ubiquitous class of prokaryotic proteins with functional roles in plasmid inheritance, environmental stress response, and cell development. ParDE family TA systems are broadly conserved on plasmids and bacterial chromosomes and have been well characterized as genetic elements that promote stable plasmid inheritance. We present a crystal structure of a chromosomally encoded ParD-ParE complex from Caulobacter crescentus at 2.6 A resolution. This TA system forms an alpha(2)beta(2) heterotetramer in the crystal and in solution. The toxin-antitoxin binding interface reveals extensive polar and hydrophobic contacts of ParD antitoxin helices with a conserved recognition and binding groove on the ParE toxin. A cross-species comparison of this complex structure with related toxin structures identified an antitoxin recognition and binding subdomain that is conserved between distantly related members of the RelE/ParE toxin superfamily despite a low level of overall primary sequence identity. We further demonstrate that ParD antitoxin is dimeric, stably folded, and largely helical when not bound to ParE toxin. Thus, the paradigmatic model in which antitoxin undergoes a disorder-to-order transition upon toxin binding does not apply to this chromosomal ParD-ParE TA system.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxin protein parE-1
A, B
110Caulobacter crescentus (strain ATCC 19089 / CB15)Gene Names: parE1
Find proteins for Q9A9T8 (Caulobacter crescentus (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9A9T8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antitoxin protein parD-1
C, D
88Caulobacter crescentus (strain ATCC 19089 / CB15)Gene Names: parD1
Find proteins for P58091 (Caulobacter crescentus (strain ATCC 19089 / CB15))
Go to UniProtKB:  P58091
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.735α = 90.00
b = 72.707β = 90.00
c = 76.814γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
ADSCdata collection
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance