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TitleMolecular mechanism of substrate transport by human peroxisomal ABCD3.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 52, Page e2513928122, Year 2025
Publish dateDec 30, 2025
AuthorsMeghna Gupta / Nitesh Kumar Khandelwal / Devin J Seka / Sree Ganesh Balasubramani / Miles Sasha Dickinson / Alexander Myasnikov / Ignacia Echeverria / Robert M Stroud /
PubMed AbstractATP-binding cassette transporters of the D subfamily (ABCD1-3) mediate the export of CoA thioesters of fatty acids from the cytosol into peroxisomes for further oxidation. ABCD3 facilitates the ...ATP-binding cassette transporters of the D subfamily (ABCD1-3) mediate the export of CoA thioesters of fatty acids from the cytosol into peroxisomes for further oxidation. ABCD3 facilitates the transport of a broad spectrum of substrates, including branched-chain fatty acids, very long-chain fatty acids, bile salt intermediates, and dicarboxylic acids as CoA adducts. Mutations in ABCD3 are associated with defects in congenital bile acid synthesis. Despite its importance, the basis for substrate selectivity and the mechanism of transport by ABCD3 are not well defined. We report the cryogenic sample electron microscopy (cryo-EM) structures of full-length human ABCD3 in its apo state and bound to one of its physiological substrates (phytanoyl-CoA) at resolutions of 3.33 Å and 3.13 Å, respectively. Our biochemical assays reveal that substrate binding induces ATPase activity in ABCD3, suggesting a substrate-dependent conformational change. Structural comparison of the apo and substrate-bound states demonstrates that the substrate interaction brings nucleotide-binding domains closer together, providing a mechanistic basis of substrate-induced ATPase activity. These findings offer critical insights into the transport mechanism of ABCD3 and lay a structural foundation for understanding its role in peroxisomal metabolite import and related diseases.
External linksProc Natl Acad Sci U S A / PubMed:41428872 / PubMed Central
MethodsEM (single particle)
Resolution3.13 - 3.33 Å
Structure data

49386

9ngj

EMDB-49386, PDB-9ngj:
CryoEM structure of human ABCD3 bound to Phytanoyl-CoA
Method: EM (single particle) / Resolution: 3.13 Å

49388

9ngm

EMDB-49388, PDB-9ngm:
CryoEM structure of human ABCD3
Method: EM (single particle) / Resolution: 3.33 Å

Chemicals

PDB-1can:
CRYSTALLOGRAPHIC STUDIES OF THE BINDING OF PROTONATED AND UNPROTONATED INHIBITORS TO CARBONIC ANHYDRASE USING HYDROGEN SULPHIDE AND NITRATE ANIONS

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / ABC transporter / Peroxisome / Fatty-acid transport / MEMBRANE PROTEIN

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