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P25045

- LCB1_YEAST

UniProt

P25045 - LCB1_YEAST

Protein

Serine palmitoyltransferase 1

Gene

LCB1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 133 (01 Oct 2014)
      Sequence version 2 (01 Feb 1996)
      Previous versions | rss
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    Functioni

    Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine.2 Publications

    Catalytic activityi

    Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.4 Publications

    Cofactori

    Pyridoxal phosphate.

    Pathwayi

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. pyridoxal phosphate binding Source: InterPro
    3. serine C-palmitoyltransferase activity Source: SGD

    GO - Biological processi

    1. sphingolipid biosynthetic process Source: SGD

    Keywords - Molecular functioni

    Acyltransferase, Transferase

    Keywords - Biological processi

    Lipid metabolism, Sphingolipid metabolism

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:YMR296C-MONOMER.
    YEAST:YMR296C-MONOMER.
    ReactomeiREACT_189220. Sphingolipid de novo biosynthesis.
    UniPathwayiUPA00222.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Serine palmitoyltransferase 1 (EC:2.3.1.50)
    Short name:
    SPT 1
    Short name:
    SPT1
    Alternative name(s):
    Long chain base biosynthesis protein 1
    Gene namesi
    Name:LCB1
    Synonyms:END8, TSC2
    Ordered Locus Names:YMR296C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIII

    Organism-specific databases

    CYGDiYMR296c.
    SGDiS000004911. LCB1.

    Subcellular locationi

    GO - Cellular componenti

    1. integral component of membrane Source: UniProtKB-KW
    2. serine C-palmitoyltransferase complex Source: SGD
    3. SPOTS complex Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Endoplasmic reticulum, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi24 – 263YLW → DRS: No effect on stability. No effect on LCB2 stabilization. 1 Publication
    Mutagenesisi50 – 8536Missing: No effect on stability. No effect on LCB2 stabilization. 1 PublicationAdd
    BLAST
    Mutagenesisi66 – 683YGI → DVK: No effect on stability. No effect on LCB2 stabilization. 1 Publication
    Mutagenesisi180 – 1801C → W or Y: Loss of activity. No effect on interaction with LCB2. 2 Publications
    Mutagenesisi191 – 1911V → D: Loss of activity. No effect on interaction with LCB2. 2 Publications
    Mutagenesisi342 – 37130Missing: Unstable. Destabilizes LCB2. 1 PublicationAdd
    BLAST
    Mutagenesisi371 – 38616Missing: No effect on stability. Destabilizes LCB2. 1 PublicationAdd
    BLAST
    Mutagenesisi386 – 41631Missing: Unstable. Destabilizes LCB2. 1 PublicationAdd
    BLAST
    Mutagenesisi416 – 42510Missing: No effect on stability. Destabilizes LCB2. 1 Publication
    Mutagenesisi433 – 45826Missing: Unstable. Destabilizes LCB2. 1 PublicationAdd
    BLAST
    Mutagenesisi549 – 5502IL → AS: No effect on stability. Partially stabilizes LCB2. 1 Publication
    Mutagenesisi549 – 5502IL → PR: No effect on stability. Partially stabilizes LCB2. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 558558Serine palmitoyltransferase 1PRO_0000163856Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei121 – 1211Phosphothreonine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP25045.
    PaxDbiP25045.
    PeptideAtlasiP25045.

    Expressioni

    Gene expression databases

    GenevestigatoriP25045.

    Interactioni

    Subunit structurei

    LCB1 and LCB2 encode essential subunits of the enzyme and form a heterodimer. Component of the SPOTS complex, at least composed of LCB1/2 (LCB1 and/or LCB2), ORM1/2 (ORM1 and/or ORM2), SAC1 and TSC3. Interacts with LCB2 and TSC3.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    LCB2P409709EBI-10059,EBI-10067

    Protein-protein interaction databases

    BioGridi35476. 167 interactions.
    DIPiDIP-5249N.
    IntActiP25045. 8 interactions.
    MINTiMINT-524207.
    STRINGi4932.YMR296C.

    Structurei

    3D structure databases

    ProteinModelPortaliP25045.
    SMRiP25045. Positions 92-450.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 4949Lumenal1 PublicationAdd
    BLAST
    Topological domaini85 – 341257Cytoplasmic1 PublicationAdd
    BLAST
    Topological domaini372 – 42453Lumenal1 PublicationAdd
    BLAST
    Topological domaini458 – 558101Cytoplasmic1 PublicationAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei50 – 8435HelicalAdd
    BLAST
    Transmembranei342 – 37130HelicalAdd
    BLAST
    Transmembranei425 – 45733HelicalAdd
    BLAST

    Family & Domainsi

    Domaini

    The first transmembrane domain is not required for stability, membrane association, interaction with LCB2, or enzymatic activity. The second and third transmembrane domains are required for stability and interaction with LCB2.

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG0156.
    GeneTreeiENSGT00550000074872.
    HOGENOMiHOG000216602.
    KOiK00654.
    OMAiDLVEEWQ.
    OrthoDBiEOG7XPZG0.

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    InterProiIPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view]
    PfamiPF00155. Aminotran_1_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    P25045-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAHIPEVLPK SIPIPAFIVT TSSYLWYYFN LVLTQIPGGQ FIVSYIKKSH    50
    HDDPYRTTVE IGLILYGIIY YLSKPQQKKS LQAQKPNLSP QEIDALIEDW 100
    EPEPLVDPSA TDEQSWRVAK TPVTMEMPIQ NHITITRNNL QEKYTNVFNL 150
    ASNNFLQLSA TEPVKEVVKT TIKNYGVGAC GPAGFYGNQD VHYTLEYDLA 200
    QFFGTQGSVL YGQDFCAAPS VLPAFTKRGD VIVADDQVSL PVQNALQLSR 250
    STVYYFNHND MNSLECLLNE LTEQEKLEKL PAIPRKFIVT EGIFHNSGDL 300
    APLPELTKLK NKYKFRLFVD ETFSIGVLGA TGRGLSEHFN MDRATAIDIT 350
    VGSMATALGS TGGFVLGDSV MCLHQRIGSN AYCFSACLPA YTVTSVSKVL 400
    KLMDSNNDAV QTLQKLSKSL HDSFASDDSL RSYVIVTSSP VSAVLHLQLT 450
    PAYRSRKFGY TCEQLFETMS ALQKKSQTNK FIEPYEEEEK FLQSIVDHAL 500
    INYNVLITRN TIVLKQETLP IVPSLKICCN AAMSPEELKN ACESVKQSIL 550
    ACCQESNK 558
    Length:558
    Mass (Da):62,207
    Last modified:February 1, 1996 - v2
    Checksum:i9F7F93E4B2C70FDB
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti443 – 4431A → P in AAA34739. (PubMed:2066332)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M63674 Genomic DNA. Translation: AAA34739.1.
    X80836 Genomic DNA. Translation: CAA56805.1.
    AY693052 Genomic DNA. Translation: AAT93071.1.
    BK006946 Genomic DNA. Translation: DAA10197.1.
    PIRiA43667.
    RefSeqiNP_014025.1. NM_001182805.1.

    Genome annotation databases

    EnsemblFungiiYMR296C; YMR296C; YMR296C.
    GeneIDi855342.
    KEGGisce:YMR296C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M63674 Genomic DNA. Translation: AAA34739.1 .
    X80836 Genomic DNA. Translation: CAA56805.1 .
    AY693052 Genomic DNA. Translation: AAT93071.1 .
    BK006946 Genomic DNA. Translation: DAA10197.1 .
    PIRi A43667.
    RefSeqi NP_014025.1. NM_001182805.1.

    3D structure databases

    ProteinModelPortali P25045.
    SMRi P25045. Positions 92-450.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35476. 167 interactions.
    DIPi DIP-5249N.
    IntActi P25045. 8 interactions.
    MINTi MINT-524207.
    STRINGi 4932.YMR296C.

    Proteomic databases

    MaxQBi P25045.
    PaxDbi P25045.
    PeptideAtlasi P25045.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YMR296C ; YMR296C ; YMR296C .
    GeneIDi 855342.
    KEGGi sce:YMR296C.

    Organism-specific databases

    CYGDi YMR296c.
    SGDi S000004911. LCB1.

    Phylogenomic databases

    eggNOGi COG0156.
    GeneTreei ENSGT00550000074872.
    HOGENOMi HOG000216602.
    KOi K00654.
    OMAi DLVEEWQ.
    OrthoDBi EOG7XPZG0.

    Enzyme and pathway databases

    UniPathwayi UPA00222 .
    BioCyci MetaCyc:YMR296C-MONOMER.
    YEAST:YMR296C-MONOMER.
    Reactomei REACT_189220. Sphingolipid de novo biosynthesis.

    Miscellaneous databases

    NextBioi 979082.
    PROi P25045.

    Gene expression databases

    Genevestigatori P25045.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    InterProi IPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view ]
    Pfami PF00155. Aminotran_1_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of LCB1, a Saccharomyces gene required for biosynthesis of the long-chain base component of sphingolipids."
      Buede R., Rinker-Schaffer C., Pinto W.J., Lester R.L., Dickson R.C.
      J. Bacteriol. 173:4325-4332(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "The LCB2 gene of Saccharomyces and the related LCB1 gene encode subunits of serine palmitoyltransferase, the initial enzyme in sphingolipid synthesis."
      Nagiec M.M., Baltisberger J.A., Wells G.B., Lester R.L., Dickson R.C.
      Proc. Natl. Acad. Sci. U.S.A. 91:7899-7902(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME ACTIVITY, SUBUNIT.
    6. "Tsc3p is an 80-amino acid protein associated with serine palmitoyltransferase and required for optimal enzyme activity."
      Gable K., Slife H., Bacikova D., Monaghan E., Dunn T.M.
      J. Biol. Chem. 275:7597-7603(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME ACTIVITY, INTERACTION WITH LCB2 AND TSC3, SUBCELLULAR LOCATION.
    7. "Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase."
      Gable K., Han G., Monaghan E., Bacikova D., Natarajan M., Williams R., Dunn T.M.
      J. Biol. Chem. 277:10194-10200(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME ACTIVITY, SUBUNIT, INTERACTION WITH LCB2, MUTAGENESIS OF CYS-180 AND VAL-191.
    8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. Cited for: ENZYME ACTIVITY, INTERACTION WITH LCB2, SUBCELLULAR LOCATION, TOPOLOGY, TRANSMEMBRANE DOMAINS, MUTAGENESIS OF 24-TYR--TRP-26; 50-ALA--THR-85; 66-TYR--ILE-68; 342-LEU--ARG-371; 371-ARG--HIS-386; 386-HIS--SER-416; 416-SER--TYR-425; 433-GLN--THR-458 AND 549-ILE-LEU-550.
    11. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-121, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    12. Cited for: IDENTIFICATION IN THE SPOTS COMPLEX.

    Entry informationi

    Entry nameiLCB1_YEAST
    AccessioniPrimary (citable) accession number: P25045
    Secondary accession number(s): D6W0C3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 133 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 22400 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    External Data

    Dasty 3