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Structure paper

TitleStructural insights into the regulation of human serine palmitoyltransferase complexes.
Journal, issue, pagesNat Struct Mol Biol, Vol. 28, Issue 3, Page 240-248, Year 2021
Publish dateFeb 8, 2021
AuthorsYingdi Wang / Yiming Niu / Zhe Zhang / Kenneth Gable / Sita D Gupta / Niranjanakumari Somashekarappa / Gongshe Han / Hongtu Zhao / Alexander G Myasnikov / Ravi C Kalathur / Teresa M Dunn / Chia-Hsueh Lee /
PubMed AbstractSphingolipids are essential lipids in eukaryotic membranes. In humans, the first and rate-limiting step of sphingolipid synthesis is catalyzed by the serine palmitoyltransferase holocomplex, which ...Sphingolipids are essential lipids in eukaryotic membranes. In humans, the first and rate-limiting step of sphingolipid synthesis is catalyzed by the serine palmitoyltransferase holocomplex, which consists of catalytic components (SPTLC1 and SPTLC2) and regulatory components (ssSPTa and ORMDL3). However, the assembly, substrate processing and regulation of the complex are unclear. Here, we present 8 cryo-electron microscopy structures of the human serine palmitoyltransferase holocomplex in various functional states at resolutions of 2.6-3.4 Å. The structures reveal not only how catalytic components recognize the substrate, but also how regulatory components modulate the substrate-binding tunnel to control enzyme activity: ssSPTa engages SPTLC2 and shapes the tunnel to determine substrate specificity. ORMDL3 blocks the tunnel and competes with substrate binding through its amino terminus. These findings provide mechanistic insights into sphingolipid biogenesis governed by the serine palmitoyltransferase complex.
External linksNat Struct Mol Biol / PubMed:33558761
MethodsEM (single particle)
Resolution2.6 - 3.4 Å
Structure data

EMDB-22598, PDB-7k0i:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-22599, PDB-7k0j:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa protomer
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-22600, PDB-7k0k:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa, 3KS-bound
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-22601, PDB-7k0l:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa, myriocin-bound
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-22602, PDB-7k0m:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-22604, PDB-7k0n:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 2
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-22605, PDB-7k0o:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 3
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-22606, PDB-7k0p:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 4
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-22608, PDB-7k0q:
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, myriocin-bound
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

ChemComp-VSD:
3-Dehydrosphinganine

ChemComp-VRP:
Myriocin / antibiotic, inhibitor*YM / Myriocin

Source
  • homo sapiens (human)
KeywordsBinding Sites / Biocatalysis / Catalytic Domain / Cryoelectron Microscopy / Humans / Ligands / Membrane Proteins / Models, Molecular / Mutation / ORMDL3 protein, human / Reproducibility of Results / SPTLC1 protein, human / SPTLC2 protein, human / Serine C-Palmitoyltransferase / Substrate Specificity / ssSPTa / MEMBRANE PROTEIN / Sphingolipid

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