5N6M

Structure of the membrane integral lipoprotein N-acyltransferase Lnt from P. aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis.

Wiktor, M.Weichert, D.Howe, N.Huang, C.Y.Olieric, V.Boland, C.Bailey, J.Vogeley, L.Stansfeld, P.J.Buddelmeijer, N.Wang, M.Caffrey, M.

(2017) Nat Commun 8: 15952-15952

  • DOI: 10.1038/ncomms15952
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipoproteins serve essential roles in the bacterial cell envelope. The posttranslational modification pathway leading to lipoprotein synthesis involves three enzymes. All are potential targets for the development of new antibiotics. Here we report th ...

    Lipoproteins serve essential roles in the bacterial cell envelope. The posttranslational modification pathway leading to lipoprotein synthesis involves three enzymes. All are potential targets for the development of new antibiotics. Here we report the crystal structure of the last enzyme in the pathway, apolipoprotein N-acyltransferase, Lnt, responsible for adding a third acyl chain to the lipoprotein's invariant diacylated N-terminal cysteine. Structures of Lnt from Pseudomonas aeruginosa and Escherichia coli have been solved; they are remarkably similar. Both consist of a membrane domain on which sits a globular periplasmic domain. The active site resides above the membrane interface where the domains meet facing into the periplasm. The structures are consistent with the proposed ping-pong reaction mechanism and suggest plausible routes by which substrates and products enter and leave the active site. While Lnt may present challenges for antibiotic development, the structures described should facilitate design of therapeutics with reduced off-target effects.


    Organizational Affiliation

    Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apolipoprotein N-acyltransferase
A
531Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: lnt (cutE)
EC: 2.3.1.269
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
N-acyltransferases
Protein: 
Lnt apoplipoprotein N-acyltransferase
Find proteins for Q9ZI86 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9ZI86
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 152.730α = 90.00
b = 39.230β = 116.26
c = 102.250γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Org. Science Foundation IrelandIrelandGrant number: 12/IA/1255

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Experimental preparation, Structure summary