Crystal structure of the antibacterial peptide ABC transporter McjD in an outward occluded state

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state.

Choudhury, H.G.Tong, Z.Mathavan, I.Li, Y.Iwata, S.Zirah, S.Rebuffat, S.van Veen, H.W.Beis, K.

(2014) Proc Natl Acad Sci U S A 111: 9145

  • DOI: https://doi.org/10.1073/pnas.1320506111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Enterobacteriaceae produce antimicrobial peptides for survival under nutrient starvation. Microcin J25 (MccJ25) is an antimicrobial peptide with a unique lasso topology. It is secreted by the ATP-binding cassette (ABC) exporter McjD, which ensures self-immunity of the producing strain through efficient export of the toxic mature peptide from the cell. Here we have determined the crystal structure of McjD from Escherichia coli at 2.7-Å resolution, which is to the authors' knowledge the first structure of an antibacterial peptide ABC transporter. Our functional and biochemical analyses demonstrate McjD-dependent immunity to MccJ25 through efflux of the peptide. McjD can directly bind MccJ25 and displays a basal ATPase activity that is stimulated by MccJ25 in both detergent solution and proteoliposomes. McjD adopts a new conformation, termed nucleotide-bound outward occluded. The new conformation defines a clear cavity; mutagenesis and ligand binding studies of the cavity have identified Phe86, Asn134, and Asn302 as important for recognition of MccJ25. Comparisons with the inward-open MsbA and outward-open Sav1866 structures show that McjD has structural similarities with both states without the intertwining of transmembrane (TM) helices. The occluded state is formed by rotation of TMs 1 and 2 toward the equivalent TMs of the opposite monomer, unlike Sav1866 where they intertwine with TMs 3-6 of the opposite monomer. Cysteine cross-linking studies on the McjD dimer in inside-out membrane vesicles of E. coli confirmed the presence of the occluded state. We therefore propose that the outward-occluded state represents a transition intermediate between the outward-open and inward-open conformation of ABC exporters.

  • Organizational Affiliation

    Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom;Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Chilton OX11 0DE, United Kingdom;Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microcin-J25 export ATP-binding/permease protein McjD
A, B
580Escherichia coliMutation(s): 0 
Gene Names: mcjD
Membrane Entity: Yes 
Find proteins for Q9X2W0 (Escherichia coli)
Explore Q9X2W0 
Go to UniProtKB:  Q9X2W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X2W0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.83α = 90
b = 107.92β = 90
c = 232.96γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary