5FGN

Integral membrane protein lipooligosaccharide phosphoethanolamine transferase A (EptA) from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a lipid A phosphoethanolamine transferase suggests how conformational changes govern substrate binding.

Anandan, A.Evans, G.L.Condic-Jurkic, K.O'Mara, M.L.John, C.M.Phillips, N.J.Jarvis, G.A.Wills, S.S.Stubbs, K.A.Moraes, I.Kahler, C.M.Vrielink, A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 2218-2223

  • DOI: 10.1073/pnas.1612927114

  • PubMed Abstract: 
  • Multidrug-resistant (MDR) gram-negative bacteria have increased the prevalence of fatal sepsis in modern times. Colistin is a cationic antimicrobial peptide (CAMP) antibiotic that permeabilizes the bacterial outer membrane (OM) and has been used to t ...

    Multidrug-resistant (MDR) gram-negative bacteria have increased the prevalence of fatal sepsis in modern times. Colistin is a cationic antimicrobial peptide (CAMP) antibiotic that permeabilizes the bacterial outer membrane (OM) and has been used to treat these infections. The OM outer leaflet is comprised of endotoxin containing lipid A, which can be modified to increase resistance to CAMPs and prevent clearance by the innate immune response. One type of lipid A modification involves the addition of phosphoethanolamine to the 1 and 4' headgroup positions by phosphoethanolamine transferases. Previous structural work on a truncated form of this enzyme suggested that the full-length protein was required for correct lipid substrate binding and catalysis. We now report the crystal structure of a full-length lipid A phosphoethanolamine transferase from Neisseria meningitidis , determined to 2.75-Å resolution. The structure reveals a previously uncharacterized helical membrane domain and a periplasmic facing soluble domain. The domains are linked by a helix that runs along the membrane surface interacting with the phospholipid head groups. Two helices located in a periplasmic loop between two transmembrane helices contain conserved charged residues and are implicated in substrate binding. Intrinsic fluorescence, limited proteolysis, and molecular dynamics studies suggest the protein may sample different conformational states to enable the binding of two very different- sized lipid substrates. These results provide insights into the mechanism of endotoxin modification and will aid a structure-guided rational drug design approach to treating multidrug-resistant bacterial infections.


    Organizational Affiliation

    School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia; alice.vrielink@uwa.edu.au.,Membrane Protein Laboratory, Diamond Light Source, Didcot OX11 0DE, United Kingdom.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143.,Research Complex at Harwell Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom.,Department of Laboratory Medicine, University of California, San Francisco, CA 94121.,Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, CA 94121.,Marshall Center for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia.,Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia.,School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lipooligosaccharide phosphoethanolamine transferase A
A
550Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Phosphoethanolamine (PEA) Transferases
Protein: 
Lipid A phosphoethanolamine transferase
Find proteins for Q7DD94 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q7DD94
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGL
Query on BGL

Download SDF File 
Download CCD File 
A
B-2-OCTYLGLUCOSIDE
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.214 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 187.285α = 90.00
b = 187.285β = 90.00
c = 205.125γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP 1003697
National Health and Medical Research Council (Australia)AustraliaAPP 1078642

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2017-03-08
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Data collection