Lcb2 (Scs1/Tsc1) is the catalytic, pyridoxal 5'-phosphate-bearing subunit 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. Lcb2 forms an obligate heterodimer with the homologous non-catalytic subunit Lcb1, and the enzyme is part of the SPOTS complex with the activator Tsc3, the Orm1/Orm2 negative regulators and the phosphatase Sac1, which couples SPT activity to sphingolipid homeostasis. LCB2 is essential; lcb2 mutants are long-chain-base auxotrophs lacking SPT activity. Lcb2 is the orthologue of human SPTLC2/SPTLC3 and is the target of the inhibitor myriocin.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004758 serine C-palmitoyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA for serine C-palmitoyltransferase activity. Lcb2 carries the PLP-binding lysine (Lys366) and is the catalytic subunit of the obligate Lcb1-Lcb2 heterodimer. 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/LCB2/LCB2-uniprot.txt Catalytic subunit 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. Lcb2 carries the PLP-binding lysine (Lys366) and is the catalytic subunit of the obligate Lcb1-Lcb2 heterodimer. Supporting Evidence: file:yeast/LCB2/LCB2-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. Lcb2 carries the PLP-binding lysine (Lys366) and is the catalytic subunit of the obligate Lcb1-Lcb2 heterodimer. 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. Lcb2 carries the PLP-binding lysine (Lys366) and is the catalytic subunit of the obligate Lcb1-Lcb2 heterodimer. 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. Lcb2 carries the PLP-binding lysine (Lys366) and is the catalytic subunit of the obligate Lcb1-Lcb2 heterodimer. 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 Lcb1 (P25045) from Gable et al. 2000 co-immunoprecipitation. '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 Lcb1 (P25045) 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 Lcb1 (P25045) 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 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:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: IPI with Lcb1 (P25045) from Michaelis et al. 2023 affinity-enrichment MS. '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). Technically true (ER lies within the cytoplasm) but uninformative and suggests a soluble pool; Lcb2 is an ER membrane protein. Supporting Evidence: file:yeast/LCB2/LCB2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum. Membrane |
| 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). 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 | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping (SL-0095) to ER; correct. Supporting Evidence: file:yeast/LCB2/LCB2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum. Membrane 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/LCB2/LCB2-uniprot.txt Catalytic subunit of serine palmitoyltransferase (SPT), which |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping to membrane (SL-0162). Correct but less specific than ER; SPT is membrane-associated. Supporting Evidence: PMID:10713067 serine palmitoyltransferase is a membrane-associated enzyme composed of at least two subunits, Lcb1p and Lcb2p. |
| GO:0016740 transferase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro IPR001917 (aminotransferase class-II PLP attachment site) mapping to the generic 'transferase activity'. Correct but uninformative; the specific activity is serine C-palmitoyltransferase. Proposed replacements: serine C-palmitoyltransferase activity 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:0017059 serine palmitoyltransferase complex | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA (PTN000343811, SPTLC2 clade) for SPT complex membership. 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:0017059 serine palmitoyltransferase complex | IDA PMID:20182505 Orm family proteins mediate sphingolipid homeostasis. | ACCEPT | Summary: Breslow et al. 2010 purified the SPOTS complex containing Lcb1, Lcb2, Tsc3, Orm1/2 and Sac1. 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: both LCB1 and LCB2 are needed for SPT; Lcb2 acts within the heterodimeric complex. is_active_in is odd for a complex term but the biology 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 Lcb2 with the SPOTS components (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 (J Bacteriol 174:2565): lcb2 strains are long-chain-base auxotrophs; LCB2 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 | IMP PMID:1556076 Characterization of enzymatic synthesis of sphingolipid long... | ACCEPT | Summary: Pinto et al. 1992 (J Bacteriol 174:2575): lcb2 membranes lack SPT activity, the essential first step of sphingolipid synthesis. 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:0030148 sphingolipid biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA for sphingolipid biosynthesis; Lcb2 catalyses the committed 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 | ACCEPT | Summary: InterPro IPR004839 mapping to PLP binding. Lcb2 carries the conserved Schiff-base lysine (Lys366, by similarity) that binds the PLP cofactor of SPT. 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'. S. cerevisiae does not make sphingosine (sphing-4-enine); its long-chain bases are dihydrosphingosine and phytosphingosine. SPT does catalyse the first step of long-chain-base synthesis, so replace with the generic sphingoid biosynthetic process. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN000343811 · PANTHER ancestral node PTN000343811 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 catalyses the first dedicated step of de novo ceramide synthesis. 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. Lcb2 is the regulated catalytic target of Orm1/2-mediated homeostatic control in the SPOTS complex; the regulators are Orm1/2. 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 |
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Experiment: Use cryo-EM of the yeast SPOTS complex in phosphorylated and unphosphorylated Orm states to visualise conformational effects on the Lcb2 PLP site.
Serine palmitoyltransferase component; responsible along with Lcb1p 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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