Lcb1 (Tsc2/End8) is one of the two large subunits of serine palmitoyltransferase (SPT), the ER-membrane enzyme that condenses L-serine with palmitoyl-CoA to form 3-ketosphinganine, the committed and rate-limiting step of sphingolipid synthesis in Saccharomyces cerevisiae. Lcb1 and Lcb2 are homologous members of the PLP-dependent alpha-oxoamine synthase family and form an obligate heterodimer in which Lcb2 carries the PLP-binding lysine; each subunit is unstable without the other. Lcb1 is a multi-pass ER membrane protein whose second and third transmembrane segments are needed for stability and Lcb2 interaction. SPT associates with the small activator Tsc3, the negative regulators Orm1/Orm2 and the phosphoinositide phosphatase Sac1 in the SPOTS complex, through which TORC2-Ypk1 signalling and Orm phosphorylation tune sphingolipid flux. LCB1 is essential; lcb1 mutants are long-chain-base auxotrophs. Lcb1 is the orthologue of human SPTLC1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004758 serine C-palmitoyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA for serine C-palmitoyltransferase activity. Lcb1 is the non-catalytic partner of the obligate Lcb1-Lcb2 heterodimer (Lcb2 carries the PLP-binding Lys366); the activity requires both subunits, so the core function is recorded as contributes_to. Supporting Evidence: PMID:8058731 The first and committed step in synthesis of the ceramide moiety of sphingolipids is catalyzed by serine palmitoyltransferase (EC 2.3.1.50), which condenses palmitoyl-CoA and serine to form 3-ketosphinganine. file:yeast/LCB1/LCB1-uniprot.txt Component of serine palmitoyltransferase (SPT), which |
| GO:0004758 serine C-palmitoyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Rhea/EC 2.3.1.50 mapping from the UniProt catalytic-activity annotation. Lcb1 is the non-catalytic partner of the obligate Lcb1-Lcb2 heterodimer (Lcb2 carries the PLP-binding Lys366); the activity requires both subunits, so the core function is recorded as contributes_to. Supporting Evidence: file:yeast/LCB1/LCB1-uniprot.txt Reaction=L-serine + hexadecanoyl-CoA + H(+) = 3-oxosphinganine + CO2 + PMID:1556076 Membrane preparations from both lcb1 and lcb2 mutant strains exhibited negligible SPT activity when tested in vitro. |
| GO:0004758 serine C-palmitoyltransferase activity | IMP PMID:1556076 Characterization of enzymatic synthesis of sphingolipid long... | ACCEPT | Summary: Pinto et al. 1992: membranes from lcb1 and lcb2 long-chain-base auxotrophs lack SPT activity in vitro. Lcb1 is the non-catalytic partner of the obligate Lcb1-Lcb2 heterodimer (Lcb2 carries the PLP-binding Lys366); the activity requires both subunits, so the core function is recorded as contributes_to. Supporting Evidence: PMID:1556076 Membrane preparations from both lcb1 and lcb2 mutant strains exhibited negligible SPT activity when tested in vitro. PMID:1556076 We conclude that the Lcb- phenotype of these mutants results from a missing or defective SPT, an activity controlled by both the LCB1 and LCB2 genes. |
| GO:0004758 serine C-palmitoyltransferase activity | IMP PMID:8058731 The LCB2 gene of Saccharomyces and the related LCB1 gene enc... | ACCEPT | Summary: Nagiec et al. 1994: SPT overproduction requires co-expression of both LCB1 and LCB2, arguing both encode SPT subunits. Lcb1 is the non-catalytic partner of the obligate Lcb1-Lcb2 heterodimer (Lcb2 carries the PLP-binding Lys366); the activity requires both subunits, so the core function is recorded as contributes_to. Supporting Evidence: PMID:8058731 Here we demonstrate that overproduction in Saccharomyces cerevisiae requires expression of LCB1, a previously isolated yeast gene, and LCB2, the isolation and characterization of which we describe. PMID:8058731 Several lines of evidence argue that both genes encode subunits of the enzyme |
| GO:0004758 serine C-palmitoyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA for the SPT step (L-serine + palmitoyl-CoA -> 3-dehydrosphinganine, EC 2.3.1.50) in SPHINGOLIPID-SYN-PWY-1. Correct reaction assignment. Lcb1 is the non-catalytic partner of the obligate Lcb1-Lcb2 heterodimer (Lcb2 carries the PLP-binding Lys366); the activity requires both subunits, so the core function is recorded as contributes_to. Supporting Evidence: PMID:8058731 The first and committed step in synthesis of the ceramide moiety of sphingolipids is catalyzed by serine palmitoyltransferase (EC 2.3.1.50), which condenses palmitoyl-CoA and serine to form 3-ketosphinganine. |
| GO:0005515 protein binding | IPI PMID:10713067 Tsc3p is an 80-amino acid protein associated with serine pal... | REMOVE | Summary: IPI with Lcb2 (P40970) from Gable et al. 2000 co-immunoprecipitation; Lcb1p and Lcb2p bind tightly to each other. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:10713067 Tsc3p coimmunoprecipitates with Lcb1p and/or Lcb2p but does not bind as tightly as Lcb1p and Lcb2p bind to each other. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: IPI with Lcb2 (P40970) from the Gavin et al. 2006 TAP-MS complex survey. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:16429126 Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification |
| GO:0005515 protein binding | IPI PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | REMOVE | Summary: IPI with Lcb2 (P40970) from Breslow et al. 2010 SPOTS complex purification. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:20182505 Purification of 3×Flag-Lcb1 yielded the same components seen in the Orm1/2 pull-downs |
| GO:0005515 protein binding | IPI PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | REMOVE | Summary: IPI with Orm1 (P53224) from Breslow et al. 2010. The Orm-SPT interaction is a regulatory one: Orm1/2 are negative regulators acting on Lcb1/2, so any regulator MF belongs on Orm1/2. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:20182505 Mass spectrometry showed that this complex comprises the serine palmitoyltransferase proteins Lcb1, Lcb2 and Tsc3, in addition to the phosphoinositide phosphatase Sac1 PMID:20182505 Additionally, our data suggest that Orm1/2 negatively regulate sphingolipid synthesis by acting directly on Lcb1/2 |
| GO:0005515 protein binding | IPI PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | REMOVE | Summary: IPI with Orm2 (Q06144) from Breslow et al. 2010; regulatory interaction as above. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:20182505 Mass spectrometry showed that this complex comprises the serine palmitoyltransferase proteins Lcb1, Lcb2 and Tsc3, in addition to the phosphoinositide phosphatase Sac1 |
| GO:0005515 protein binding | IPI PMID:20212121 Orm1 and Orm2 are conserved endoplasmic reticulum membrane p... | REMOVE | Summary: IPI with Orm1 (P53224) from Han et al. 2010, who showed Orm1/2 physically interact with SPT. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:20212121 Physical interaction between Orm1 and Orm2 and serine palmitoyltransferase, responsible for the first committed step in sphingolipid synthesis, further supports a role for the Orm proteins in regulating sphingolipid synthesis. |
| GO:0005515 protein binding | IPI PMID:20212121 Orm1 and Orm2 are conserved endoplasmic reticulum membrane p... | REMOVE | Summary: IPI with Orm2 (Q06144) from Han et al. 2010. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:20212121 Physical interaction between Orm1 and Orm2 and serine palmitoyltransferase, responsible for the first committed step in sphingolipid synthesis, further supports a role for the Orm proteins in regulating sphingolipid synthesis. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: IPI with Lcb2 (P40970) from the Michaelis et al. 2023 affinity-enrichment MS interactome. 'Protein binding' is uninformative; the meaningful content (membership of the serine palmitoyltransferase/SPOTS complex) is captured by GO:0017059. Removed per the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:37968396 Here we develop a sensitive high-throughput method using highly reproducible affinity enrichment coupled to mass spectrometry |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: UniProt SubCell 'Cytoplasm' mapping (SL-0086), no evidence code given. Technically true (the ER lies within the cytoplasm) but uninformative and liable to be read as a soluble pool; Lcb1 is an integral ER membrane protein (also annotated). Supporting Evidence: file:yeast/LCB1/LCB1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum membrane; Multi- |
| GO:0005783 endoplasmic reticulum | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | ACCEPT | Summary: ER localisation from the SWAT N-terminal GFP endomembrane library (Yofe et al. 2016); consistent with SPT being an ER membrane enzyme. Supporting Evidence: PMID:26928762 we constructed and investigated a library of ∼1,800 strains carrying SWAT-GFP modules at the amino termini of endomembrane proteins PMID:10713067 serine palmitoyltransferase is a membrane-associated enzyme composed of at least two subunits, Lcb1p and Lcb2p. |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA (PTN000343996, SPTLC1 clade). The ER is the conserved site of SPT in eukaryotes. Supporting Evidence: PMID:10713067 serine palmitoyltransferase is a membrane-associated enzyme composed of at least two subunits, Lcb1p and Lcb2p. |
| GO:0005783 endoplasmic reticulum | IDA PMID:1556076 Characterization of enzymatic synthesis of sphingolipid long... | ACCEPT | Summary: Pinto et al. 1992 measured SPT activity in crude membrane preparations; curator IDA for ER. Consistent with the established ER location. Supporting Evidence: PMID:1556076 SPT activity was demonstrated in vitro with crude membrane preparations from S. cerevisiae |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping (SL-0097): Lcb1 is a multi-pass ER membrane protein; most precise location. Supporting Evidence: file:yeast/LCB1/LCB1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum membrane; Multi- PMID:10713067 serine palmitoyltransferase is a membrane-associated enzyme composed of at least two subunits, Lcb1p and Lcb2p. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA compartment assignment (SPHINGOLIPID-SYN-PWY-1) to cytosol. SPT is a multi-pass integral ER membrane heterodimer; GO places membrane-embedded enzymes in the membrane, not in the cytosol (which excludes membranes). This is a pathway-level default, not evidence for a cytosolic pool. Supporting Evidence: PMID:10713067 serine palmitoyltransferase is a membrane-associated enzyme composed of at least two subunits, Lcb1p and Lcb2p. |
| GO:0006665 sphingolipid metabolic process | IEA GO_REF:0000041 | TOO GENERAL | Summary: UniPathway mapping (UPA00222 sphingolipid metabolism). Correct but broad. Supporting Evidence: file:yeast/LCB1/LCB1-uniprot.txt Component of serine palmitoyltransferase (SPT), which |
| GO:0017059 serine palmitoyltransferase complex | IDA PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | ACCEPT | Summary: Breslow et al. 2010 purified Lcb1 with Lcb2, Tsc3, Orm1/2 and Sac1 (SPOTS complex). GO:0017059 explicitly includes Lcb1/Lcb2 as catalytic components and Tsc3/Orm1/2 as regulators. Supporting Evidence: PMID:20182505 Mass spectrometry showed that this complex comprises the serine palmitoyltransferase proteins Lcb1, Lcb2 and Tsc3, in addition to the phosphoinositide phosphatase Sac1 PMID:20182505 Together, these results establish that Orm proteins are components of a novel and conserved protein complex, which we term the SPOTS complex (Serine Palmitoyltransferase, Orm1/2, Tsc3, and Sac1). |
| GO:0017059 serine palmitoyltransferase complex | IMP PMID:8058731 The LCB2 gene of Saccharomyces and the related LCB1 gene enc... | ACCEPT | Summary: Nagiec et al. 1994: LCB1 and LCB2 encode SPT subunits; the activity requires both. The is_active_in qualifier is odd for a complex term, but the biology (Lcb1 acts within the SPT complex) is correct. Supporting Evidence: PMID:8058731 Here we demonstrate that overproduction in Saccharomyces cerevisiae requires expression of LCB1, a previously isolated yeast gene, and LCB2, the isolation and characterization of which we describe. |
| GO:0017059 serine palmitoyltransferase complex | IPI PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | ACCEPT | Summary: Co-purification of Lcb1 with Lcb2/Tsc3/Orm/Sac1 (Breslow et al. 2010). Supporting Evidence: PMID:20182505 Mass spectrometry showed that this complex comprises the serine palmitoyltransferase proteins Lcb1, Lcb2 and Tsc3, in addition to the phosphoinositide phosphatase Sac1 |
| GO:0030148 sphingolipid biosynthetic process | IMP PMID:1556075 Sphingolipid long-chain-base auxotrophs of Saccharomyces cer... | ACCEPT | Summary: Pinto et al. 1992: lcb1 mutants are long-chain-base auxotrophs and lose phosphoinositol sphingolipid synthesis; LCB1 acts at the first step of long-chain-base synthesis. Supporting Evidence: PMID:1556075 it is likely that the LCB1 and LCB2 genes are involved in the first step of long-chain-base synthesis. |
| GO:0030148 sphingolipid biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA for sphingolipid biosynthesis; SPT catalyses the committed first step. Supporting Evidence: PMID:20182505 LCB1 and LCB2 encode serine palmitoyltransferase, an essential hetero-dimeric enzyme that catalyzes the first and rate-limiting step in sphingolipid biosynthesis |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro IPR004839 (aminotransferase class I/II) mapping to pyridoxal phosphate binding. Lcb1 has the fold but, unlike Lcb2, has no annotated PLP-binding (Schiff-base) lysine; in the SPT heterodimer the PLP cofactor is attached to Lcb2 (Lys366). Domain-based transfer of cofactor binding to the non-catalytic subunit is not supported. Supporting Evidence: file:yeast/LCB2/LCB2-uniprot.txt N6-(pyridoxal phosphate)lysine |
| GO:0046512 sphingosine biosynthetic process | IBA GO_REF:0000033 | MODIFY | Summary: PANTHER IBA for 'sphingosine biosynthetic process'. GO:0046512 refers specifically to sphingosine (sphing-4-enine), which S. cerevisiae does not make (its long-chain bases are dihydrosphingosine and phytosphingosine). SPT does catalyse the first step of long-chain-base synthesis, so the essence is right; replace with the generic sphingoid biosynthetic process. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN000343996 · PANTHER ancestral node PTN000343996 SUPPORTS SOURCE BUT NOT TARGET Node annotation reflects vertebrate/plant SPT making sphingosine precursors; S. cerevisiae lacks the delta-4 desaturase and makes no sphingosine, so the sphingosine-specific child term does not transfer; the generic sphingoid term does. Proposed replacements: sphingoid biosynthetic process Supporting Evidence: PMID:1556075 it is likely that the LCB1 and LCB2 genes are involved in the first step of long-chain-base synthesis. PMID:8058731 The first and committed step in synthesis of the ceramide moiety of sphingolipids is catalyzed by serine palmitoyltransferase (EC 2.3.1.50), which condenses palmitoyl-CoA and serine to form 3-ketosphinganine. |
| GO:0046513 ceramide biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA for ceramide biosynthetic process. SPT forms 3-ketosphinganine, the first dedicated intermediate of de novo ceramide synthesis, so it carries out a step of that process. Supporting Evidence: PMID:8058731 The first and committed step in synthesis of the ceramide moiety of sphingolipids is catalyzed by serine palmitoyltransferase (EC 2.3.1.50), which condenses palmitoyl-CoA and serine to form 3-ketosphinganine. |
| GO:0090156 intracellular sphingolipid homeostasis | NAS PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | KEEP AS NON CORE | Summary: NAS from Breslow et al. 2010 for intracellular sphingolipid homeostasis. SPT is the enzyme whose activity is homeostatically tuned by Orm1/2 phosphorylation within the SPOTS complex; the homeostatic control is exerted by Orm1/2 (and Ypk1), with Lcb1 as the regulated target. Retained as non-core. Supporting Evidence: PMID:20182505 Additionally, our data suggest that Orm1/2 negatively regulate sphingolipid synthesis by acting directly on Lcb1/2 PMID:20182505 Together, these results establish that Orm proteins are components of a novel and conserved protein complex, which we term the SPOTS complex (Serine Palmitoyltransferase, Orm1/2, Tsc3, and Sac1). |
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Download this section (compressed HTML)Q: Does Lcb1 contribute catalytic residues to the shared active site at the Lcb1-Lcb2 dimer interface, as in bacterial homodimeric SPT, or is its role purely structural and regulatory (Orm/Tsc3 docking)?
Experiment: Reconstitute purified Lcb1-Lcb2-Tsc3 with interface point mutants in Lcb1 and measure kcat/Km for serine and palmitoyl-CoA to map Lcb1 residues contributing to catalysis.
Component of serine palmitoyltransferase; responsible along with Lcb2p for the first committed step in sphingolipid synthesis, which is the condensation of serine with palmitoyl-CoA to form 3-ketosphinganine
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