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P40970

- LCB2_YEAST

UniProt

P40970 - LCB2_YEAST

Protein

Serine palmitoyltransferase 2

Gene

LCB2

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 135 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Catalytic subunit 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.

    Catalytic activityi

    Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.5 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:YDR062W-MONOMER.
    YEAST:YDR062W-MONOMER.
    ReactomeiREACT_189220. Sphingolipid de novo biosynthesis.
    UniPathwayiUPA00222.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Serine palmitoyltransferase 2 (EC:2.3.1.50)
    Short name:
    SPT 2
    Alternative name(s):
    Long chain base biosynthesis protein 2
    Gene namesi
    Name:LCB2
    Synonyms:SCS1, TSC1
    Ordered Locus Names:YDR062W
    ORF Names:D4246, YD9609.16
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDR062w.
    SGDiS000002469. LCB2.

    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
    Mutagenesisi334 – 3341H → F: Loss of activity. No effect on interaction with LCB1. 1 Publication
    Mutagenesisi366 – 3661K → T: Loss of activity. No effect on interaction with LCB1. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 561561Serine palmitoyltransferase 2PRO_0000163862Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei366 – 3661N6-(pyridoxal phosphate)lysineBy similarity

    Proteomic databases

    MaxQBiP40970.
    PaxDbiP40970.
    PeptideAtlasiP40970.

    Expressioni

    Gene expression databases

    GenevestigatoriP40970.

    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 LCB1 and TSC3.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    LCB1P250459EBI-10067,EBI-10059

    Protein-protein interaction databases

    BioGridi32117. 65 interactions.
    DIPiDIP-6658N.
    IntActiP40970. 31 interactions.
    MINTiMINT-616393.
    STRINGi4932.YDR062W.

    Structurei

    3D structure databases

    ProteinModelPortaliP40970.
    SMRiP40970. Positions 158-522.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei57 – 7721HelicalSequence AnalysisAdd
    BLAST
    Transmembranei443 – 46321HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG0156.
    GeneTreeiENSGT00550000074678.
    HOGENOMiHOG000206826.
    KOiK00654.
    OMAiPEPGGCC.
    OrthoDBiEOG7XPZG0.

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
    IPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PfamiPF00155. Aminotran_1_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 1 hit.
    PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P40970-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE    50
    PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNKH LDLLEHDGLA 100
    PWFSNFESFY VRRIKMRIDD CFSRPTTGVP GRFIRCIDRI SHNINEYFTY 150
    SGAVYPCMNL SSYNYLGFAQ SKGQCTDAAL ESVDKYSIQS GGPRAQIGTT 200
    DLHIKAEKLV ARFIGKEDAL VFSMGYGTNA NLFNAFLDKK CLVISDELNH 250
    TSIRTGVRLS GAAVRTFKHG DMVGLEKLIR EQIVLGQPKT NRPWKKILIC 300
    AEGLFSMEGT LCNLPKLVEL KKKYKCYLFI DEAHSIGAMG PTGRGVCEIF 350
    GVDPKDVDIL MGTFTKSFGA AGGYIAADQW IIDRLRLDLT TVSYSESMPA 400
    PVLAQTISSL QTISGEICPG QGTERLQRIA FNSRYLRLAL QRLGFIVYGV 450
    ADSPVIPLLL YCPSKMPAFS RMMLQRRIAV VVVAYPATPL IESRVRFCMS 500
    ASLTKEDIDY LLRHVSEVGD KLNLKSNSGK SSYDGKRQRW DIEEVIRRTP 550
    EDCKDDKYFV N 561
    Length:561
    Mass (Da):63,111
    Last modified:February 1, 1995 - v1
    Checksum:i06DF4A709CC9F29B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti5 – 62AN → PH in AAA53669. (PubMed:8063782)Curated
    Sequence conflicti23 – 231Q → P in AAA53669. (PubMed:8063782)Curated
    Sequence conflicti236 – 2361F → S in AAU09688. (PubMed:17322287)Curated
    Sequence conflicti441 – 4411Q → K in AAA53669. (PubMed:8063782)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L33931 Genomic DNA. Translation: AAA53669.1.
    M95669 Genomic DNA. Translation: AAA34740.1.
    X84162 Genomic DNA. Translation: CAA58978.1.
    Z49209 Genomic DNA. Translation: CAA89091.1.
    Z74358 Genomic DNA. Translation: CAA98880.1.
    AY723771 Genomic DNA. Translation: AAU09688.1.
    BK006938 Genomic DNA. Translation: DAA11908.1.
    PIRiS54046.
    RefSeqiNP_010347.1. NM_001180370.1.

    Genome annotation databases

    EnsemblFungiiYDR062W; YDR062W; YDR062W.
    GeneIDi851634.
    KEGGisce:YDR062W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L33931 Genomic DNA. Translation: AAA53669.1 .
    M95669 Genomic DNA. Translation: AAA34740.1 .
    X84162 Genomic DNA. Translation: CAA58978.1 .
    Z49209 Genomic DNA. Translation: CAA89091.1 .
    Z74358 Genomic DNA. Translation: CAA98880.1 .
    AY723771 Genomic DNA. Translation: AAU09688.1 .
    BK006938 Genomic DNA. Translation: DAA11908.1 .
    PIRi S54046.
    RefSeqi NP_010347.1. NM_001180370.1.

    3D structure databases

    ProteinModelPortali P40970.
    SMRi P40970. Positions 158-522.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32117. 65 interactions.
    DIPi DIP-6658N.
    IntActi P40970. 31 interactions.
    MINTi MINT-616393.
    STRINGi 4932.YDR062W.

    Proteomic databases

    MaxQBi P40970.
    PaxDbi P40970.
    PeptideAtlasi P40970.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR062W ; YDR062W ; YDR062W .
    GeneIDi 851634.
    KEGGi sce:YDR062W.

    Organism-specific databases

    CYGDi YDR062w.
    SGDi S000002469. LCB2.

    Phylogenomic databases

    eggNOGi COG0156.
    GeneTreei ENSGT00550000074678.
    HOGENOMi HOG000206826.
    KOi K00654.
    OMAi PEPGGCC.
    OrthoDBi EOG7XPZG0.

    Enzyme and pathway databases

    UniPathwayi UPA00222 .
    BioCyci MetaCyc:YDR062W-MONOMER.
    YEAST:YDR062W-MONOMER.
    Reactomei REACT_189220. Sphingolipid de novo biosynthesis.

    Miscellaneous databases

    NextBioi 969188.
    PROi P40970.

    Gene expression databases

    Genevestigatori P40970.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProi IPR001917. Aminotrans_II_pyridoxalP_BS.
    IPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view ]
    Pfami PF00155. Aminotran_1_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 1 hit.
    PROSITEi PS00599. AA_TRANSFER_CLASS_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Suppressors of the Ca(2+)-sensitive yeast mutant (csg2) identify genes involved in sphingolipid biosynthesis. Cloning and characterization of SCS1, a gene required for serine palmitoyltransferase activity."
      Zhao C., Beeler T., Dunn T.
      J. Biol. Chem. 269:21480-21488(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ENZYME ACTIVITY.
    2. "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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ENZYME ACTIVITY, SUBUNIT.
      Strain: ATCC 26109 / X2180.
    3. "Nucleotide sequence analysis of a 32,500 bp region of the right arm of Saccharomyces cerevisiae chromosome IV."
      Brandt P., Ramlow S., Otto B., Bloecker H.
      Yeast 12:85-90(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    6. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    7. "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 LCB1 AND TSC3, SUBCELLULAR LOCATION.
    8. "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: ENZYME ACTIVITY, INTERACTION WITH LCB1, SUBUNIT, MUTAGENESIS OF HIS-334 AND LYS-366.
    9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. Cited for: ENZYME ACTIVITY, INTERACTION WITH LCB1, SUBCELLULAR LOCATION.
    12. Cited for: IDENTIFICATION IN THE SPOTS COMPLEX.

    Entry informationi

    Entry nameiLCB2_YEAST
    AccessioniPrimary (citable) accession number: P40970
    Secondary accession number(s): D6VS48, Q66RG8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 135 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 54500 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 IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3