8B0L

Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with PE


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N -acyltransferase.

Smithers, L.Degtjarik, O.Weichert, D.Huang, C.Y.Boland, C.Bowen, K.Oluwole, A.Lutomski, C.Robinson, C.V.Scanlan, E.M.Wang, M.Olieric, V.Shalev-Benami, M.Caffrey, M.

(2023) Sci Adv 9: eadf5799-eadf5799

  • DOI: https://doi.org/10.1126/sciadv.adf5799
  • Primary Citation of Related Structures:  
    8AQ2, 8AQ3, 8AQ4, 8B0K, 8B0L, 8B0M, 8B0N, 8B0O, 8B0P

  • PubMed Abstract: 

    Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein N -acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects.


  • Organizational Affiliation

    School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein N-acyltransferase532Escherichia coli K-12Mutation(s): 1 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY (Subject of Investigation/LOI)
Query on PTY

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland16/IA/4435
Irish Research CouncilIrelandGOIPD/2021/40

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection