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Structure paper

TitleCryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateFeb 22, 2024
AuthorsKexin Hu / Qing Zhang / Yang Chen / Jintong Yang / Ying Xia / Bing Rao / Shaobai Li / Yafeng Shen / Mi Cao / Hongliang Lu / An Qin / Xian-Cheng Jiang / Deqiang Yao / Jie Zhao / Lu Zhou / Yu Cao /
PubMed AbstractSphingomyelin (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) ...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.
External linksNat Struct Mol Biol / PubMed:38388831
MethodsEM (single particle)
Resolution3.29 - 3.74 Å
Structure data

35492

8ijq

EMDB-35492, PDB-8ijq:
The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
Method: EM (single particle) / Resolution: 3.45 Å

35493

8ijr

EMDB-35493, PDB-8ijr:
The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine
Method: EM (single particle) / Resolution: 3.29 Å

37383

8w9w

EMDB-37383, PDB-8w9w:
The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide/phosphoethanolamine
Method: EM (single particle) / Resolution: 3.74 Å

37385

8w9y

EMDB-37385, PDB-8w9y:
The cryo-EM structure of human sphingomyelin synthase-related protein
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-16C:
N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE

ChemComp-Z0P:
(2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate

ChemComp-OPE:
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / Phosphorylethanolamine


ChemComp, No image

ChemComp-UJO:
Unknown entry

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / synthase / sphingomyelin / CPE / lipid metabolism

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