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.

鞘磷脂 (SM) 在调节哺乳动物细胞膜特性方面发挥着关键作用，并且是生物活性分子的重要库。SM 生物合成由鞘磷脂合酶 (SMS) 家族介导，该家族包括 SMS1、SMS2 和 SMS 相关 (SMSr) 成员。虽然 SMS1 和 SMS2 表现出 SMS 活性，但 SMSr 具有神经酰胺磷酸乙醇胺合酶活性。在这里，我们确定了人 SMSr 与神经酰胺、二酰甘油/磷酸乙醇胺和神经酰胺/磷酸乙醇胺 (CPE) 复合物的冷冻电子显微镜结构。该结构揭示了六聚体排列，反应室位于跨膜螺旋之间。在该结构中，发现了一个催化五元组 E-H/D-H-D，位于反应室亲脂和亲水部分之间的界面处。此外，该研究还揭示了 SMSr 催化的两步合成过程，包括 PE-PLC（磷脂酰乙醇胺-磷脂酶 C）水解以及随后将磷酸乙醇胺部分转移至神经酰胺。这项研究提供了对 SMSr 催化机制的见解，并扩展了我们对鞘脂代谢的理解。