7WLS

Crystal structure of the multidrug efflux transporter BpeB from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


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Literature

Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism.

Kato, T.Okada, U.Hung, L.W.Yamashita, E.Kim, H.B.Kim, C.Y.Terwilliger, T.C.Schweizer, H.P.Murakami, S.

(2023) Proc Natl Acad Sci U S A 120: e2215072120-e2215072120

  • DOI: https://doi.org/10.1073/pnas.2215072120
  • Primary Citation of Related Structures:  
    7WLS, 7WLV

  • PubMed Abstract: 

    BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae , where both are symmetric trimers composed of three "binding"-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.


  • Organizational Affiliation

    Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Efflux pump membrane transporter
A, B, C
1,051Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: bpeBBPSL0815
Membrane Entity: Yes 
UniProt
Find proteins for Q63WS7 (Burkholderia pseudomallei (strain K96243))
Explore Q63WS7 
Go to UniProtKB:  Q63WS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63WS7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.883α = 90
b = 135.977β = 98.21
c = 157.819γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
Cootmodel building
MolProbitymodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H02412

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description