8AYF

Crystal structure of human Sphingosine-1-phosphate lyase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dual species sphingosine-1-phosphate lyase inhibitors to combine antifungal and anti-inflammatory activities in cystic fibrosis: a feasibility study.

Cellini, B.Pampalone, G.Camaioni, E.Pariano, M.Catalano, F.Zelante, T.Dindo, M.Macchioni, L.Di Veroli, A.Galarini, R.Paoletti, F.Davidescu, M.Stincardini, C.Vascelli, G.Bellet, M.M.Saba, J.Giovagnoli, S.Giardina, G.Romani, L.Costantini, C.

(2023) Sci Rep 13: 22692-22692

  • DOI: https://doi.org/10.1038/s41598-023-50121-4
  • Primary Citation of Related Structures:  
    8AYF, 8CMX

  • PubMed Abstract: 

    Cystic fibrosis (CF) is an autosomal recessive disorder characterized by respiratory failure due to a vicious cycle of defective Cystic Fibrosis Transmembrane conductance Regulator (CFTR) function, chronic inflammation and recurrent bacterial and fungal infections. Although the recent introduction of CFTR correctors/potentiators has revolutionized the clinical management of CF patients, resurgence of inflammation and persistence of pathogens still posit a major concern and should be targeted contextually. On the background of a network-based selectivity that allows to target the same enzyme in the host and microbes with different outcomes, we focused on sphingosine-1-phosphate (S1P) lyase (SPL) of the sphingolipid metabolism as a potential candidate to uniquely induce anti-inflammatory and antifungal activities in CF. As a feasibility study, herein we show that interfering with S1P metabolism improved the immune response in a murine model of CF with aspergillosis while preventing germination of Aspergillus fumigatus conidia. In addition, in an early drug discovery process, we purified human and A. fumigatus SPL, characterized their biochemical and structural properties, and performed an in silico screening to identify potential dual species SPL inhibitors. We identified two hits behaving as competitive inhibitors of pathogen and host SPL, thus paving the way for hit-to-lead and translational studies for the development of drug candidates capable of restraining fungal growth and increasing antifungal resistance.


  • Organizational Affiliation

    Department of Medicine and Surgery, University of Perugia, P.le Lucio Severi 1, 06132, Perugia, Italy. barbara.cellini@unipg.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine-1-phosphate lyase 1
A, B
494Homo sapiensMutation(s): 0 
Gene Names: SGPL1KIAA1252
EC: 4.1.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O95470 (Homo sapiens)
Explore O95470 
Go to UniProtKB:  O95470
PHAROS:  O95470
GTEx:  ENSG00000166224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95470
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.16α = 90
b = 127.41β = 104.85
c = 66.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentItalyRP11916B407928AA
Other governmentItalyRM12117A5BDD4AEC
Other privateItalyFFC#16/2020

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-01-03
    Changes: Database references