8CRI

Crystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites.

Dienemann, J.N.Chen, S.Y.Hitzenberger, M.Sievert, M.L.Hacker, S.M.Prigge, S.T.Zacharias, M.Groll, M.Sieber, S.A.

(2023) Angew Chem Int Ed Engl 62: e202304533-e202304533

  • DOI: https://doi.org/10.1002/anie.202304533
  • Primary Citation of Related Structures:  
    8CRI, 8CRJ, 8CRL

  • PubMed Abstract: 

    The development of novel anti-infectives requires unprecedented strategies targeting pathways which are solely present in pathogens but absent in humans. Following this principle, we developed inhibitors of lipoic acid (LA) salvage, a crucial pathway for the survival of LA auxotrophic bacteria and parasites but non-essential in human cells. An LA-based probe was selectively transferred onto substrate proteins via lipoate protein ligase (LPL) in intact cells, and their binding sites were determined by mass spectrometry. Probe labeling served as a proxy of LPL activity, enabling in situ screenings for cell-permeable LPL inhibitors. Profiling a focused compound library revealed two substrate analogs (LAMe and C3) as inhibitors, which were further validated by binding studies and co-crystallography. Importantly, LAMe exhibited low toxicity in human cells and achieved killing of Plasmodium falciparum in erythrocytes with an EC 50 value of 15 μM, making it the most effective LPL inhibitor reported to date.


  • Organizational Affiliation

    Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lipoate--protein ligase
A, B
335Listeria monocytogenesMutation(s): 0 
Gene Names: 
EC: 6.3.1.20
UniProt
Find proteins for A0A1D2IX29 (Listeria monocytogenes)
Explore A0A1D2IX29 
Go to UniProtKB:  A0A1D2IX29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D2IX29
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.87α = 90
b = 72.79β = 98.04
c = 93.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection