protein C

Experimental Data Snapshot

  • Resolution: 3.00 Å

wwPDB Validation   3D Report Full Report

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Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition.

Wu, H.H.Symersky, J.Lu, M.

(2019) Commun Biol 2: 210-210

  • DOI: https://doi.org/10.1038/s42003-019-0446-y
  • Primary Citation of Related Structures:  
    6OOM, 6OOP, 6OOQ

  • PubMed Abstract: 

    MdfA is a prototypical H + -coupled multidrug transporter that is characterized by extraordinarily broad substrate specificity. The involvement of specific H-bonds in MdfA-drug interactions and the simplicity of altering the substrate specificity of MdfA contradict the promiscuous nature of multidrug recognition, presenting a baffling conundrum. Here we show the X-ray structures of MdfA variant I239T/G354E in complexes with three electrically different ligands, determined at resolutions up to 2.2 Å. Our structures reveal that I239T/G354E interacts with these compounds differently from MdfA and that I239T/G354E possesses two discrete, non-overlapping substrate-binding sites. Our results shed new light on the molecular design of multidrug-binding and protonation sites and highlight the importance of often-neglected, long-range charge-charge interactions in multidrug recognition. Beyond helping to solve the ostensible conundrum of multidrug recognition, our findings suggest the mechanistic difference between substrate and inhibitor for any H + -dependent multidrug transporter, which may open new vistas on curtailing efflux-mediated multidrug resistance.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug transporter MdfA392Escherichia coliMutation(s): 0 
Gene Names: A9R57_05385BJJ90_17655
Membrane Entity: Yes 
Find proteins for P0AEY8 (Escherichia coli (strain K12))
Explore P0AEY8 
Go to UniProtKB:  P0AEY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEY8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DXC (Subject of Investigation/LOI)
Query on DXC

Download Ideal Coordinates CCD File 
C24 H40 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.477α = 90
b = 71.369β = 109.73
c = 113.142γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-09-04 
  • Deposition Author(s): Lu, M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094195

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence