Crystal structure of LpSPL/Lpp2128, Legionella pneumophila sphingosine-1 phosphate lyase

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.265 

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This is version 2.0 of the entry. See complete history


Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy.

Rolando, M.Escoll, P.Nora, T.Botti, J.Boitez, V.Bedia, C.Daniels, C.Abraham, G.Stogios, P.J.Skarina, T.Christophe, C.Dervins-Ravault, D.Cazalet, C.Hilbi, H.Rupasinghe, T.W.Tull, D.McConville, M.J.Ong, S.Y.Hartland, E.L.Codogno, P.Levade, T.Naderer, T.Savchenko, A.Buchrieser, C.

(2016) Proc Natl Acad Sci U S A 113: 1901-1906

  • DOI: https://doi.org/10.1073/pnas.1522067113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Autophagy is an essential component of innate immunity, enabling the detection and elimination of intracellular pathogens. Legionella pneumophila, an intracellular pathogen that can cause a severe pneumonia in humans, is able to modulate autophagy through the action of effector proteins that are translocated into the host cell by the pathogen's Dot/Icm type IV secretion system. Many of these effectors share structural and sequence similarity with eukaryotic proteins. Indeed, phylogenetic analyses have indicated their acquisition by horizontal gene transfer from a eukaryotic host. Here we report that L. pneumophila translocates the effector protein sphingosine-1 phosphate lyase (LpSpl) to target the host sphingosine biosynthesis and to curtail autophagy. Our structural characterization of LpSpl and its comparison with human SPL reveals high structural conservation, thus supporting prior phylogenetic analysis. We show that LpSpl possesses S1P lyase activity that was abrogated by mutation of the catalytic site residues. L. pneumophila triggers the reduction of several sphingolipids critical for macrophage function in an LpSpl-dependent and -independent manner. LpSpl activity alone was sufficient to prevent an increase in sphingosine levels in infected host cells and to inhibit autophagy during macrophage infection. LpSpl was required for efficient infection of A/J mice, highlighting an important virulence role for this effector. Thus, we have uncovered a previously unidentified mechanism used by intracellular pathogens to inhibit autophagy, namely the disruption of host sphingolipid biosynthesis.

  • Organizational Affiliation

    Institut Pasteur, Biologie des Bactéries Intracellulaires, 75724 Paris, France; CNRS UMR 3525, 75724 Paris, France;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable sphingosine-1-phosphate lyase
A, B
551Legionella pneumophila str. ParisMutation(s): 0 
Gene Names: lpp2128
Find proteins for Q5X3A8 (Legionella pneumophila (strain Paris))
Explore Q5X3A8 
Go to UniProtKB:  Q5X3A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5X3A8
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.783α = 90
b = 118.252β = 114.38
c = 57.794γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2016-02-17
    Changes: Data collection
  • Version 1.3: 2016-03-02
    Changes: Database references
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2024-03-13
    Changes: Atomic model, Data collection