5N6H

Structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ncomms15952
  • Primary Citation of Related Structures:  
    5N6H, 5N6L, 5N6M

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein N-acyltransferase
A, B
532Escherichia coli K-12Mutation(s): 0 
Gene Names: lntcutEb0657JW0654
EC: 2.3.1 (PDB Primary Data), 2.3.1.269 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P23930 (Escherichia coli (strain K12))
Explore P23930 
Go to UniProtKB:  P23930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23930
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.2α = 90
b = 142.3β = 90
c = 199.92γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
BUSTERrefinement
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Org. Science Foundation IrelandIreland12/IA/1255

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references