Abstract
Sphingomyelin (SM) has key roles in modulating mammalian membrane properties and serves as an important pool for bioactive molecules. SM biosynthesis is mediated by the sphingomyelin synthase (SMS) family, comprising SMS1, SMS2 and SMS-related (SMSr) members. Although SMS1 and SMS2 exhibit SMS activity, SMSr possesses ceramide phosphoethanolamine synthase activity. Here we determined the cryo-electron microscopic structures of human SMSr in complexes with ceramide, diacylglycerol/phosphoethanolamine and ceramide/phosphoethanolamine (CPE). The structures revealed a hexameric arrangement with a reaction chamber located between the transmembrane helices. Within this structure, a catalytic pentad E–H/D–H–D was identified, situated at the interface between the lipophilic and hydrophilic segments of the reaction chamber. Additionally, the study unveiled the two-step synthesis process catalyzed by SMSr, involving PE–PLC (phosphatidylethanolamine–phospholipase C) hydrolysis and the subsequent transfer of the phosphoethanolamine moiety to ceramide. This research provides insights into the catalytic mechanism of SMSr and expands our understanding of sphingolipid metabolism.
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Data availability
The coordinates are deposited in the Protein Data Bank (PDB) with accession codes 8W9Y, 8IJQ, 8IJR and 8W9W. The cryo-EM maps have been deposited in the Electron Microscopy Data Bank (EMDB) with accession codes EMD-37385, EMD-35492, EMD-35493 and EMD-37383. Other relevant data generated in this study are provided in the Supplementary Information and Source Data files. Source data are provided with this paper.
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Acknowledgements
We thank M. Lei, D. Ye and L. Wang for scientific discussion and R. Liao for assistance with the data analysis. This work was supported by National Natural Science Foundation of China (grants 82072468 and 82272519 to Y.C.), National Key Research and Development Program of China (grant 2018YFC1004704 to Y.C.), Shanghai Municipal Committee of Science and Technology (grants. 20S11902000 to Y.C. and 21TQ016 to L.Z.), SHIPM-pi fund (grant JY201804 to Y.C. and J.Z.) from Shanghai Institute of Precision Medicine, the Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine. This work was also supported by the Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System (A.Q. and J.Z.) and the Innovative Research Team of High-level Local Universities (grant SHSMU-ZLCX20211700 to Y.C.) from the Shanghai Municipal Education Commission. We thank the staff members of the Electron Microimaging Center, Bioimaging Facility and Proteomics Platform at Shanghai Institute of Precision Medicine for providing technical support and assistance in data collection.
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Y.C. and L.Z. conceived the study. Y.C., L.Z., K.H., Q.Z., B.R., Y.Ch, D.Y., A.Q., J.Z. and S.L. designed the experiments. K.H., Q.Z., Y.X., H.L. and J.Y. performed the biochemical assay. Q.Z., K.H., M.C., Y.S. and Y.C. performed structural biology experiments. Y.C. and D.Y. built and refined structural models. Y.C., K.H., Q.Z., D.Y., J.Y., L.Z., J.Z. and X.J. wrote the manuscript.
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Nature Structural & Molecular Biology thanks Yongchan Lee and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Sara Osman, in collaboration with the Nature Structural & Molecular Biology team. Peer reviewer reports are available.
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Hu, K., Zhang, Q., Chen, Y. et al. Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis. Nat Struct Mol Biol (2024). https://doi.org/10.1038/s41594-024-01237-2
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DOI: https://doi.org/10.1038/s41594-024-01237-2
