3HPW

CcdB dimer in complex with one C-terminal CcdA domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.452 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rejuvenation of CcdB-Poisoned Gyrase by an Intrinsically Disordered Protein Domain.

De Jonge, N.Garcia-Pino, A.Buts, L.Haesaerts, S.Charlier, D.Zangger, K.Wyns, L.De Greve, H.Loris, R.

(2009) Mol.Cell 35: 154-163

  • DOI: 10.1016/j.molcel.2009.05.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toxin-antitoxin modules are small regulatory circuits that ensure survival of bacterial populations under challenging environmental conditions. The ccd toxin-antitoxin module on the F plasmid codes for the toxin CcdB and its antitoxin CcdA. CcdB pois ...

    Toxin-antitoxin modules are small regulatory circuits that ensure survival of bacterial populations under challenging environmental conditions. The ccd toxin-antitoxin module on the F plasmid codes for the toxin CcdB and its antitoxin CcdA. CcdB poisons gyrase while CcdA actively dissociates CcdB:gyrase complexes in a process called rejuvenation. The CcdA:CcdB ratio modulates autorepression of the ccd operon. The mechanisms behind both rejuvenation and regulation of expression are poorly understood. We show that CcdA binds consecutively to two partially overlapping sites on CcdB, which differ in affinity by six orders of magnitude. The first, picomolar affinity interaction triggers a conformational change in CcdB that initiates the dissociation of CcdB:gyrase complexes by an allosteric segmental binding mechanism. The second, micromolar affinity binding event regulates expression of the ccd operon. Both functions of CcdA, rejuvenation and autoregulation, are mechanistically intertwined and depend crucially on the intrinsically disordered nature of the CcdA C-terminal domain.


    Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytotoxic protein ccdB
A, B
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ccdB (G, letB, letD)
Find proteins for P62554 (Escherichia coli (strain K12))
Go to UniProtKB:  P62554
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein ccdA
C
36Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ccdA (H, letA)
Find proteins for P62552 (Escherichia coli (strain K12))
Go to UniProtKB:  P62552
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.452 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.357α = 90.00
b = 38.038β = 97.51
c = 69.651γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
ADSCdata collection
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance