3QDR

Structural characterization of the interaction of colicin A, colicin N, and TolB with the TolAIII translocon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Evidence That Colicin A Protein Binds to a Novel Binding Site of TolA Protein in Escherichia coli Periplasm.

Li, C.Zhang, Y.Vankemmelbeke, M.Hecht, O.Aleanizy, F.S.Macdonald, C.Moore, G.R.James, R.Penfold, C.N.

(2012) J.Biol.Chem. 287: 19048-19057

  • DOI: 10.1074/jbc.M112.342246
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Tol assembly of proteins is an interacting network of proteins located in the Escherichia coli cell envelope that transduces energy and contributes to cell integrity. TolA is central to this network linking the inner and outer membranes by intera ...

    The Tol assembly of proteins is an interacting network of proteins located in the Escherichia coli cell envelope that transduces energy and contributes to cell integrity. TolA is central to this network linking the inner and outer membranes by interactions with TolQ, TolR, TolB, and Pal. Group A colicins, such as ColA, parasitize the Tol network through interactions with TolA and/or TolB to facilitate translocation through the cell envelope to reach their cytotoxic site of action. We have determined the first structure of the C-terminal domain of TolA (TolAIII) bound to an N-terminal ColA polypeptide (TA(53-107)). The interface region of the TA(53-107)-TolAIII complex consists of polar contacts linking residues Arg-92 to Arg-96 of ColA with residues Leu-375-Pro-380 of TolA, which constitutes a β-strand addition commonly seen in more promiscuous protein-protein contacts. The interface region also includes three cation-π interactions (Tyr-58-Lys-368, Tyr-90-Lys-379, Phe-94-Lys-396), which have not been observed in any other colicin-Tol protein complex. Mutagenesis of the interface residues of ColA or TolA revealed that the effect on the interaction was cumulative; single mutations of either partner had no effect on ColA activity, whereas mutations of three or more residues significantly reduced ColA activity. Mutagenesis of the aromatic ring component of the cation-π interacting residues showed Tyr-58 of ColA to be essential for the stability of complex formation. TA(53-107) binds on the opposite side of TolAIII to that used by g3p, ColN, or TolB, illustrating the flexible nature of TolA as a periplasmic hub protein.


    Organizational Affiliation

    School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein tolA
A
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tolA (cim, excC, lky)
Find proteins for P19934 (Escherichia coli (strain K12))
Go to UniProtKB:  P19934
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin-A
B
63Citrobacter freundiiMutation(s): 0 
Gene Names: caa
Find proteins for P04480 (Citrobacter freundii)
Go to UniProtKB:  P04480
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.497α = 90.00
b = 119.624β = 90.00
c = 30.147γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
XDSdata reduction
PHASESphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-01-19 
  • Released Date: 2012-01-25 
  • Deposition Author(s): Li, C.

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-05-09
    Type: Database references
  • Version 1.2: 2012-06-20
    Type: Database references