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TitleMolecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2).
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 7755, Year 2023
Publish dateNov 27, 2023
AuthorsJingbo Yi / Boya Qi / Jian Yin / Ruochong Li / Xudong Chen / Junhan Hu / Guohui Li / Sensen Zhang / Yuebin Zhang / Maojun Yang /
PubMed AbstractEnzymatic breakdown of sphingomyelin by sphingomyelinase (SMase) is the main source of the membrane lipids, ceramides, which are involved in many cellular physiological processes. However, the full- ...Enzymatic breakdown of sphingomyelin by sphingomyelinase (SMase) is the main source of the membrane lipids, ceramides, which are involved in many cellular physiological processes. However, the full-length structure of human neutral SMase has not been resolved; therefore, its catalytic mechanism remains unknown. Here, we resolve the structure of human full-length neutral SMase, sphingomyelinase 1 (SMPD2), which reveals that C-terminal transmembrane helices contribute to dimeric architecture of hSMPD2 and that D111 - K116 loop domain is essential for substrate hydrolysis. Coupled with molecular docking, we clarify the binding pose of sphingomyelin, and site-directed mutagenesis further confirms key residues responsible for sphingomyelin binding. Hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamic (MD) simulations are utilized to elaborate the catalysis of hSMPD2 with the reported in vitro substrates, sphingomyelin and lyso-platelet activating fator (lyso-PAF). Our study provides mechanistic details that enhance our knowledge of lipid metabolism and may lead to an improved understanding of ceramide in disease and in cancer treatment.
External linksNat Commun / PubMed:38012235 / PubMed Central
MethodsEM (single particle)
Resolution3.07 Å
Structure data

35948

8j2f

EMDB-35948, PDB-8j2f:
Human neutral shpingomyelinase
Method: EM (single particle) / Resolution: 3.07 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HP6:
HEPTANE / Heptane

ChemComp-C14:
TETRADECANE / Tetradecane

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / enzyme

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