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TitleCollaborative regulation of yeast SPT-Orm2 complex by phosphorylation and ceramide.
Journal, issue, pagesCell Rep, Vol. 43, Issue 2, Page 113717, Year 2024
Publish dateJan 28, 2024
AuthorsTian Xie / Feitong Dong / Gongshe Han / Xinyue Wu / Peng Liu / Zike Zhang / Jianlong Zhong / Somashekarappa Niranjanakumari / Kenneth Gable / Sita D Gupta / Wenchen Liu / Peter J Harrison / Dominic J Campopiano / Teresa M Dunn / Xin Gong /
PubMed AbstractThe homeostatic regulation of serine palmitoyltransferase (SPT) activity in yeast involves N-terminal phosphorylation of Orm proteins, while higher eukaryotes lack these phosphorylation sites. ...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.
External linksCell Rep / PubMed:38285738
MethodsEM (single particle)
Resolution3.1 Å
Structure data

35304

8iaj

EMDB-35304, PDB-8iaj:
Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A) complex
Method: EM (single particle) / Resolution: 3.1 Å

35306

8iak

EMDB-35306, PDB-8iak:
Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A-N71A) complex
Method: EM (single particle) / Resolution: 3.1 Å

35310

8iam

EMDB-35310, PDB-8iam:
Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3D) complex
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

ChemComp-Z1T:
N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • Saccharomyces cerevisiae S288C
  • saccharomyces cerevisiae s288c (yeast)
  • arabidopsis thaliana (thale cress)
KeywordsTRANSFERASE/INHIBITOR / ceramide / phosphorylation / TRANSFERASE-INHIBITOR COMPLEX

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