8IAJ

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A) complex

Summary for 8IAJ

• Entry DOI: 10.2210/pdb8iaj/pdb
• EMDB information: 35304
• Descriptor: chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1, Serine palmitoyltransferase 2, Protein ORM2, ... (6 entities in total)
• Functional Keywords: ceramide, phosphorylation, transferase-inhibitor complex, transferase/inhibitor
• Biological source: Arabidopsis thaliana; More
• Total number of polymer chains: 8
• Total formula weight: 315724.94

Authors

Xie, T.,Gong, X. (deposition date: 2023-02-08, release date: 2024-02-14)

Primary citation

Xie, T.,Dong, F.,Han, G.,Wu, X.,Liu, P.,Zhang, Z.,Zhong, J.,Niranjanakumari, S.,Gable, K.,Gupta, S.D.,Liu, W.,Harrison, P.J.,Campopiano, D.J.,Dunn, T.M.,Gong, X.
Collaborative regulation of yeast SPT-Orm2 complex by phosphorylation and ceramide.
Cell Rep, 43:113717-113717, 2024

PubMed Abstract: The homeostatic regulation of serine palmitoyltransferase (SPT) activity in yeast involves N-terminal phosphorylation of Orm proteins, while higher eukaryotes lack these phosphorylation sites. Although recent studies have indicated a conserved ceramide-mediated feedback inhibition of the SPT-ORM/ORMDL complex in higher eukaryotes, its conservation and relationship with phosphorylation regulation in yeast remain unclear. Here, we determine the structure of the yeast SPT-Orm2 complex in a dephosphomimetic state and identify an evolutionarily conserved ceramide-sensing site. Ceramide stabilizes the dephosphomimetic Orm2 in an inhibitory conformation, facilitated by an intramolecular β-sheet between the N- and C-terminal segments of Orm2. Moreover, we find that a phosphomimetic mutant of Orm2, positioned adjacent to its intramolecular β-sheet, destabilizes the inhibitory conformation of Orm2. Taken together, our findings suggest that both Orm dephosphorylation and ceramide binding are crucial for suppressing SPT activity in yeast. This highlights a distinctive regulatory mechanism in yeast involving the collaborative actions of phosphorylation and ceramide.

PubMed: 38285738
DOI: 10.1016/j.celrep.2024.113717

Experimental method

ELECTRON MICROSCOPY (3.1 Å)