5JMN

Fusidic acid bound AcrB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB.

Oswald, C.Tam, H.K.Pos, K.M.

(2016) Nat Commun 7: 13819-13819

  • DOI: 10.1038/ncomms13819

  • PubMed Abstract: 
  • The deployment of multidrug efflux pumps is a powerful defence mechanism for Gram-negative bacterial cells when exposed to antimicrobial agents. The major multidrug efflux transport system in Escherichia coli, AcrAB-TolC, is a tripartite system using ...

    The deployment of multidrug efflux pumps is a powerful defence mechanism for Gram-negative bacterial cells when exposed to antimicrobial agents. The major multidrug efflux transport system in Escherichia coli, AcrAB-TolC, is a tripartite system using the proton-motive force as an energy source. The polyspecific substrate-binding module AcrB uses various pathways to sequester drugs from the periplasm and outer leaflet of the inner membrane. Here we report the asymmetric AcrB structure in complex with fusidic acid at a resolution of 2.5 Å and mutational analysis of the putative fusidic acid binding site at the transmembrane domain. A groove shaped by the interface between transmembrane helix 1 (TM1) and TM2 specifically binds fusidic acid and other lipophilic carboxylated drugs. We propose that these bound drugs are actively displaced by an upward movement of TM2 towards the AcrB periplasmic porter domain in response to protonation events in the transmembrane domain.


    Organizational Affiliation

    Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multidrug efflux pump subunit AcrB
A, B, C
1057Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acrB (acrE)
Membrane protein
mpstruc
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DARPin
D, E
169N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETE
Query on ETE

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A, C
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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B, C
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
P3G
Query on P3G

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B
3,6,9,12,15-PENTAOXAHEPTADECANE
C12 H26 O5
HYDWALOBQJFOMS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
D12
Query on D12

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B, C
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUA
Query on FUA

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A, B, C
FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
PTY
Query on PTY

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B, C
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
LMT
Query on LMT

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A, B, C
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
D10
Query on D10

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B
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

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A, C
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 145.654α = 90.00
b = 163.248β = 90.00
c = 246.042γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB807 (Transport and Communication across Biological Membranes
German Research FoundationGermanyDFG EXC115 (Cluster of Excellence Frankfurt Macromolecular Complexes)

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references
  • Version 1.2: 2017-01-11
    Type: Database references