1T9X

Structural Basis of Multidrug Transport by the AcrB Multidrug Efflux Pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Periplasmic Drug-Binding Site of the AcrB Multidrug Efflux Pump: a Crystallographic and Site-Directed Mutagenesis Study

Yu, E.W.Aires, J.R.McDermott, G.Nikaido, H.

(2005) J.Bacteriol. 187: 6804-6815

  • DOI: 10.1128/JB.187.19.6804-6815.2005
  • Primary Citation of Related Structures:  1T9T, 1T9U, 1T9V, 1T9W, 1T9Y

  • PubMed Abstract: 
  • The Escherichia coli AcrB multidrug efflux pump is a membrane protein that recognizes many structurally dissimilar toxic compounds. We previously reported the X-ray structures of four AcrB-ligand complexes in which the ligands were bound to the wall ...

    The Escherichia coli AcrB multidrug efflux pump is a membrane protein that recognizes many structurally dissimilar toxic compounds. We previously reported the X-ray structures of four AcrB-ligand complexes in which the ligands were bound to the wall of the extremely large central cavity in the transmembrane domain of the pump. Genetic studies, however, suggested that discrimination between the substrates occurs mainly in the periplasmic domain rather than the transmembrane domain of the pump. We here describe the crystal structures of the AcrB mutant in which Asn109 was replaced by Ala, with five structurally diverse ligands, ethidium, rhodamine 6G, ciprofloxacin, nafcillin, and Phe-Arg-beta-naphthylamide. The ligands bind not only to the wall of central cavity but also to a new periplasmic site within the deep external depression formed by the C-terminal periplasmic loop. This depression also includes residues identified earlier as being important in the specificity. We show here that conversion into alanine of the Phe664, Phe666, or Glu673 residue in the periplasmic binding site produced significant decreases in the MIC of most agents in the N109A background. Furthermore, decreased MICs were also observed when these residues were mutated in the wild-type AcrB background, although the effects were more modest. The MIC data were also confirmed by assays of ethidium influx rates in intact cells, and our results suggest that the periplasmic binding site plays a role in the physiological process of drug efflux.


    Organizational Affiliation

    Department of Molecular and Cell Biology, 16 Barker Hall, University of California, Berkeley, CA 94720-3202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acriflavine resistance protein B
A
1049Escherichia coli (strain K12)Gene Names: acrB (acrE)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Multi-Drug Efflux Transporters
Protein: 
AcrB bacterial multi-drug efflux transporter
Find proteins for P31224 (Escherichia coli (strain K12))
Go to UniProtKB:  P31224
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ET
Query on ET

Download SDF File 
Download CCD File 
A
ETHIDIUM
C21 H20 N3
QTANTQQOYSUMLC-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.272 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 144.967α = 90.00
b = 144.967β = 90.00
c = 519.372γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance