2IVZ

Structure of TolB in complex with a peptide of the colicin E9 T- domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Competitive Recruitment of the Periplasmic Translocation Portal Tolb by a Natively Disordered Domain of Colicin E9

Loftus, S.R.Walker, D.Mate, M.J.Bonsor, D.A.James, R.Moore, G.R.Kleanthous, C.

(2006) Proc.Natl.Acad.Sci.USA 103: 12353

  • DOI: 10.1073/pnas.0603433103

  • PubMed Abstract: 
  • The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm of Escherichia coli, the latter triggering transloc ...

    The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm of Escherichia coli, the latter triggering translocation of the toxin across the OM. We have identified the 16-residue TolB binding epitope in the natively disordered T-domain of the nuclease colicin E9 (ColE9) and solved the crystal structure of the complex. ColE9 folds into a distorted hairpin within a canyon of the six-bladed beta-propeller of TolB, using two tryptophans to bolt the toxin to the canyon floor and numerous intramolecular hydrogen bonds to stabilize the bound conformation. This mode of binding enables colicin side chains to hydrogen-bond TolB residues in and around the channel that runs through the beta-propeller and that constitutes the binding site of peptidoglycan-associated lipoprotein (Pal). Pal is a globular binding partner of TolB, and their association is known to be important for OM integrity. The structure is therefore consistent with translocation models wherein the colicin disrupts the TolB-Pal complex causing local instability of the OM as a prelude to toxin import. Intriguingly, Ca(2+) ions, which bind within the beta-propeller channel and switch the surface electrostatics from negative to positive, are needed for the negatively charged T-domain to bind TolB with an affinity equivalent to that of Pal and competitively displace it. Our study demonstrates that natively disordered proteins can compete with globular proteins for binding to folded scaffolds but that this can require cofactors such as metal ions to offset unfavorable interactions.


    Related Citations: 
    • The Structure of Tolb, an Essential Component of the Tol-Dependent Translocation System, and its Protein-Protein Interaction with the Translocation Domain of Colicin E9.
      Carr, S.,Penfold, C.N.,Bamford, V.,James, R.,Hemmings, A.M.
      (2000) Structure 8: 57
    • Structure of the Escherichia Coli Tolb Protein Determined by MAD Methods at 1.95 A Resolution
      Abergel, C.,Bouveret, E.,Claverie, J.-M.,Brown, K.,Rigal, A.,Lazdunski, C.,Benedetti, H.
      (1999) Structure 7: 1291


    Organizational Affiliation

    Department of Biology (Area 10), University of York, York YO10 5YW, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN TOLB
A, B, C, D
439Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tolB
Find proteins for P0A855 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A855
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COLICIN-E9
E, F, G, H
16Escherichia coliMutation(s): 0 
Gene Names: col (cei)
EC: 3.1.-.-
Find proteins for P09883 (Escherichia coli)
Go to UniProtKB:  P09883
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 130.092α = 90.00
b = 39.933β = 110.62
c = 154.848γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance