Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA.
Nat Commun. 2023 Jun 13;14(1):3475. doi: 10.1038/s41467-023-39274-y.
The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here we show that purified human SPT-ORMDL complexes are inhibited by the central sphingolipid metabolite ceramide. We have solved the cryo-EM structure of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided mutational analyses reveal the essential function of this ceramide binding site for the suppression of SPT activity. Structural studies indicate that ceramide can induce and lock the N-terminus of ORMDL3 into an inhibitory conformation. Furthermore, we demonstrate that childhood amyotrophic lateral sclerosis (ALS) variants in the SPTLC1 subunit cause impaired ceramide sensing in the SPT-ORMDL3 mutants. Our work elucidates the molecular basis of ceramide sensing by the SPT-ORMDL complex for establishing sphingolipid homeostasis and indicates an important role of impaired ceramide sensing in disease development.
ORM/ORMDL 家族蛋白作为丝氨酸棕榈酰转移酶（SPT）复合物的调节亚基发挥作用，SPT 复合物是神经酰胺生物合成中起始和限速的酶。该复合物受到细胞神经酰胺水平的严格调控，但神经酰胺感应机制尚不清楚。本研究表明，纯化的人 SPT-ORMDL 复合物被神经酰胺代谢物中间产物神经酰胺抑制。本研究解析了结合神经酰胺的 SPT-ORMDL3 复合物的冷冻电镜结构。结构导向的突变分析揭示了该神经酰胺结合位点对 SPT 活性抑制的重要功能。结构研究表明，神经酰胺可以诱导并锁定 ORMDL3 的 N 端进入抑制构象。此外，本研究证明 SPTLC1 亚基中的儿童肌萎缩侧索硬化症（ALS）变异会导致 SPT-ORMDL3 突变体中神经酰胺感应受损。本研究阐明了 SPT-ORMDL 复合物感应神经酰胺的分子基础，以建立神经酰胺稳态，并表明神经酰胺感应受损在疾病发展中起重要作用。
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