5OFR

Structure of the antibacterial peptide ABC transporter McjD in a high energy outward occluded intermediate state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD.

Bountra, K.Hagelueken, G.Choudhury, H.G.Corradi, V.El Omari, K.Wagner, A.Mathavan, I.Zirah, S.Yuan Wahlgren, W.Tieleman, D.P.Schiemann, O.Rebuffat, S.Beis, K.

(2017) EMBO J 36: 3062-3079

  • DOI: 10.15252/embj.201797278
  • Primary Citation of Related Structures:  
    5OFP, 5OFR

  • PubMed Abstract: 
  • Certain pathogenic bacteria produce and release toxic peptides to ensure either nutrient availability or evasion from the immune system. These peptides are also toxic to the producing bacteria that utilize dedicated ABC transporters to provide self-immunity ...

    Certain pathogenic bacteria produce and release toxic peptides to ensure either nutrient availability or evasion from the immune system. These peptides are also toxic to the producing bacteria that utilize dedicated ABC transporters to provide self-immunity. The ABC transporter McjD exports the antibacterial peptide MccJ25 in Escherichia coli Our previously determined McjD structure provided some mechanistic insights into antibacterial peptide efflux. In this study, we have determined its structure in a novel conformation, apo inward-occluded and a new nucleotide-bound state, high-energy outward-occluded intermediate state, with a defined ligand binding cavity. Predictive cysteine cross-linking in E. coli membranes and PELDOR measurements along the transport cycle indicate that McjD does not undergo major conformational changes as previously proposed for multi-drug ABC exporters. Combined with transport assays and molecular dynamics simulations, we propose a novel mechanism for toxic peptide ABC exporters that only requires the transient opening of the cavity for release of the peptide. We propose that shielding of the cavity ensures that the transporter is available to export the newly synthesized peptides, preventing toxic-level build-up.


    Related Citations: 
    • 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

    Organizational Affiliation

    Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microcin-J25 export ATP-binding/permease protein McjDAB580Escherichia coliMutation(s): 0 
Gene Names: mcjD
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
McjD antimicrobial peptide transporter, high energy outward occluded intermediate state
Find proteins for Q9X2W0 (Escherichia coli)
Explore Q9X2W0 
Go to UniProtKB:  Q9X2W0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
VO4
Query on VO4

Download CCD File 
A, B
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.29α = 90
b = 105.04β = 105.55
c = 117.37γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-11 
  • Released Date: 2017-09-06 
  • Deposition Author(s): Beis, K., Bountra, K.

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N020103/1

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references