3IAX | pdb_00003iax

The crystal structure of the TolB box of Colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.257 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the TolB box of colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins.

Zhang, Y.Li, C.Vankemmelbeke, M.N.Bardelang, P.Paoli, M.Penfold, C.N.James, R.

(2009) Mol Microbiol 75: 623-636

  • DOI: https://doi.org/10.1111/j.1365-2958.2009.06808.x
  • Primary Citation Related Structures: 
    3IAX

  • PubMed Abstract: 

    Interaction of the TolB box of Group A colicins with the TolB protein in the periplasm of Escherichia coli cells promotes transport of the cytotoxic domain of the colicin across the cell envelope. The crystal structure of a complex between a 107-residue peptide (TA(1-107)) of the translocation domain of colicin A (ColA) and TolB identified the TolB box as a 12-residue peptide that folded into a distorted hairpin within a central canyon of the beta-propeller domain of TolB. Comparison of this structure with that of the colicin E9 (ColE9) TolB box-TolB complex, together with site-directed mutagenesis of the ColA TolB box residues, revealed important differences in the interaction of the two TolB boxes with an overlapping binding site on TolB. Substitution of the TolB box residues of ColA with those of ColE9 conferred the ability to competitively recruit TolB from Pal but reduced the biological activity of the mutant ColA. This datum explains (i) the difference in binding affinities of ColA and ColE9 with TolB, and (ii) the inability of ColA, unlike ColE9, to competitively recruit TolB from Pal, allowing an understanding of how these two colicins interact in a different way with a common translocation portal in E. coli cells.


  • Organizational Affiliation
    • Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.

Macromolecule Content 

  • Total Structure Weight: 59.19 kDa 
  • Atom Count: 3,175 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 553 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein tolB438Escherichia coliMutation(s): 0 
Gene Names: b0740JW5100tolBUTI89_C0736
UniProt
Find proteins for P0A855 (Escherichia coli (strain K12))
Explore P0A855 
Go to UniProtKB:  P0A855
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A855
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Colicin-A115Citrobacter freundiiMutation(s): 0 
Gene Names: caacolA
UniProt
Find proteins for P04480 (Citrobacter freundii)
Explore P04480 
Go to UniProtKB:  P04480
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04480
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.257 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.955α = 90
b = 40.174β = 97.18
c = 80.868γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2009-10-13 
  • Deposition Author(s): Li, C.

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description