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TitleMolecular basis of Spns1-mediated lysophospholipid transport from the lysosome.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 1, Page e2409596121, Year 2025
Publish dateJan 7, 2025
AuthorsHongwen Chen / Hoa T T Ha / Nadia Elghobashi-Meinhardt / Nhung A Le / Philip Schmiege / Long N Nguyen / Xiaochun Li /
PubMed AbstractSpns1 mediates the rate-limiting efflux of lysophospholipids from the lysosome to the cytosol. Deficiency of Spns1 is associated with embryonic senescence, as well as liver and skeletal muscle ...Spns1 mediates the rate-limiting efflux of lysophospholipids from the lysosome to the cytosol. Deficiency of Spns1 is associated with embryonic senescence, as well as liver and skeletal muscle atrophy in animal models. However, the mechanisms by which Spns1 transports lysophospholipid and proton sensing remain unclear. Here, we present a cryogenic electron microscopy structure of human Spns1 in lysophosphatidylcholine (LPC)-bound lumen-facing conformation. Notably, LPC snugly binds within the luminal-open cavity, where the molecular dynamics simulations reveal that LPC presents a propensity to enter between transmembrane-helices (TM) 5 and 8. Structural comparisons and cell-based transport assays uncover several pivotal residues at TM 5/8 that orchestrate the transport cycle, which are unique to Spns1. Furthermore, we identify a five-residue network that is crucial for proton-sensing by Spns1. Transference of these network residues to Spns2, a sphingosine-1-phosphate uniporter, causes the chimeric Spns2 to be low pH dependent. Our results reveal molecular insights into lysosomal LPC transport and the proton-sensing mechanism by Spns1.
External linksProc Natl Acad Sci U S A / PubMed:39739806 / PubMed Central
MethodsEM (single particle)
Resolution3.22 - 3.49 Å
Structure data

EMDB-44741: Cryo-EM structure of human Spns1
Method: EM (single particle) / Resolution: 3.49 Å

44742

9boi

EMDB-44742, PDB-9boi:
Cryo-EM structure of human Spns1 in complex with LPC (18:1)
Method: EM (single particle) / Resolution: 3.22 Å

Chemicals

ChemComp-42H:
(4R,7R,18Z)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide

Source
  • homo sapiens (human)
  • aequorea victoria (jellyfish)
  • escherichia coli (E. coli)
KeywordsMEMBRANE PROTEIN / lysosome / major facilitator superfamily / lysophospholipid transporter / lysophosphatidylcholine

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