1TQQ

Structure of TolC in complex with hexamminecobalt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug effllux protein TolC

Higgins, M.K.Eswaran, J.Edwards, P.C.Schertler, G.F.Hughes, C.Koronakis, V.

(2004) J Mol Biol 342: 697-702

  • DOI: https://doi.org/10.1016/j.jmb.2004.07.088
  • Primary Citation of Related Structures:  
    1TQQ

  • PubMed Abstract: 

    The trimeric TolC protein of Escherichia coli comprises an outer membrane beta-barrel and a contiguous alpha-helical barrel projecting across the periplasm. This provides a single 140 A long pore for multidrug efflux and protein export. We have previously reported that trivalent cations such as hexammine cobalt can severely inhibit the conductivity of the TolC pore reconstituted in planar lipid bilayers. Here, isothermal calorimetry shows that Co(NH(3))(6)(3+) binds to TolC with an affinity of 20 nM. The crystal structure of the TolC-Co(NH(3))(6)(3+) complex was determined to 2.75 A resolution, and showed no significant difference in the protein when compared with unliganded TolC. An electron density difference map revealed that a single ligand molecule binds at the centre of the periplasmic entrance, the sole constriction of TolC. The octahedral symmetry of the ligand and the three-fold rotational symmetry of the TolC entrance determine a binding site in which the ligand forms hydrogen bonds with the Asp(374) residue of each monomer. When Asp(374) was substituted by alanine, high affinity ligand binding was abolished and inhibition of TolC pore conductivity in lipid bilayers was alleviated. Comparable effects followed independent substitution of the neighbouring Asp(371), indicating that this aspartate ring also contributes to the high affinity ligand binding site. As the electronegative entrance is widely conserved in the TolC family, it may be a useful target for the development of inhibitors against multidrug resistant pathogenic bacteria.


  • Organizational Affiliation

    Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein tolC
A, B, C
471Escherichia coliMutation(s): 0 
Gene Names: TOLCMTCBMUKAREFIB3035
Membrane Entity: Yes 
UniProt
Find proteins for P02930 (Escherichia coli (strain K12))
Explore P02930 
Go to UniProtKB:  P02930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02930
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
D [auth C]COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.276α = 90
b = 265.276β = 90
c = 96.253γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description