5EG1

Antibacterial peptide ABC transporter McjD with a resolved lipid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD.

Mehmood, S.Corradi, V.Choudhury, H.G.Hussain, R.Becker, P.Axford, D.Zirah, S.Rebuffat, S.Tieleman, D.P.Robinson, C.V.Beis, K.

(2016) J.Biol.Chem. 291: 21656-21668

  • DOI: 10.1074/jbc.M116.732107

  • PubMed Abstract: 
  • The lipid bilayer is a dynamic environment that consists of a mixture of lipids with different properties that regulate the function of membrane proteins; these lipids are either annular, masking the protein hydrophobic surface, or specific lipids, e ...

    The lipid bilayer is a dynamic environment that consists of a mixture of lipids with different properties that regulate the function of membrane proteins; these lipids are either annular, masking the protein hydrophobic surface, or specific lipids, essential for protein function. In this study, using tandem mass spectrometry, we have identified specific lipids associated with the Escherichia coli ABC transporter McjD, which translocates the antibacterial peptide MccJ25. Using non-denaturing mass spectrometry, we show that McjD in complex with MccJ25 survives the gas phase. Partial delipidation of McjD resulted in reduced ATPase activity and thermostability as shown by circular dichroism, both of which could be restored upon addition of defined E. coli lipids. We have resolved a phosphatidylglycerol lipid associated with McjD at 3.4 Å resolution, whereas molecular dynamic simulations carried out in different lipid environments assessed the binding of specific lipids to McjD. Combined, our data show a synergistic effect of zwitterionic and negatively charged lipids on the activity of McjD; the zwitterionic lipids provide structural stability to McjD, whereas the negatively charged lipids are essential for its function.


    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

    From the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microcin-J25 export ATP-binding/permease protein McjD
A, B
580Escherichia coliMutation(s): 0 
Gene Names: mcjD
Find proteins for Q9X2W0 (Escherichia coli)
Go to UniProtKB:  Q9X2W0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
P6L
Query on P6L

Download SDF File 
Download CCD File 
B
(2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE
C40 H75 O10 P
WLVNRDXLPAAELE-GDRYEXQRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.980α = 90.00
b = 109.130β = 90.00
c = 233.190γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PHASERphasing
BUSTERrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/H01778X/1

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-11-16
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence