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Protein

Sphingoid long chain base kinase 5

Gene

LCB5

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the phosphorylation of the sphingoid long chain bases dihydrosphingosine (DHS or sphinganine) and phytosphingosine (PHS) to form dihydrosphingosine 1-phosphate (DHS-1P) and phytosphingosine 1-phosphate (PHS-1P) respectively. Redundant to LCB4, is only responsible for few percent of the total activity. Involved in the biosynthesis of sphingolipids and ceramides. Involved in heat-induced transient cell cycle arrest. Accumulation of phosphorylated sphingoid long chain bases (LCBPs) stimulates calcium influx and activates calcineurin signaling. Involved in heat-stress resistance.5 Publications

Catalytic activityi

ATP + sphinganine = ADP + sphinganine 1-phosphate.
ATP + phytosphingosine = ADP + phytosphingosine 1-phosphate.

Kineticsi

  1. KM=2 µM for dihydrosphingosine1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei308 – 3081ATPPROSITE-ProRule annotation
    Active sitei335 – 3351Proton donor/acceptorBy similarity
    Binding sitei340 – 3401ATPPROSITE-ProRule annotation
    Binding sitei434 – 4341ATPPROSITE-ProRule annotation
    Binding sitei440 – 4401ATPPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi276 – 2783ATPPROSITE-ProRule annotation
    Nucleotide bindingi366 – 3683ATPPROSITE-ProRule annotation
    Nucleotide bindingi652 – 6543ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • D-erythro-sphingosine kinase activity Source: SGD
    • sphinganine kinase activity Source: UniProtKB-EC

    GO - Biological processi

    • calcium-mediated signaling Source: SGD
    • response to heat Source: SGD
    • sphingolipid metabolic process Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Lipid metabolism, Sphingolipid metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:YLR260W-MONOMER.
    YEAST:YLR260W-MONOMER.
    ReactomeiREACT_307521. Glycosphingolipid metabolism.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sphingoid long chain base kinase 5 (EC:2.7.1.91)
    Short name:
    LCB kinase 5
    Alternative name(s):
    Sphinganine kinase 5
    Gene namesi
    Name:LCB5
    Ordered Locus Names:YLR260W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311 Componenti: Chromosome XII

    Organism-specific databases

    CYGDiYLR260w.
    EuPathDBiFungiDB:YLR260W.
    SGDiS000004250. LCB5.

    Subcellular locationi

    GO - Cellular componenti

    • Golgi apparatus Source: SGD
    • Golgi membrane Source: UniProtKB-SubCell
    • membrane Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Golgi apparatus, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 687687Sphingoid long chain base kinase 5PRO_0000255957Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi91 – 911S-palmitoyl cysteineBy similarity
    Lipidationi94 – 941S-palmitoyl cysteineBy similarity

    Keywords - PTMi

    Lipoprotein, Palmitate

    Proteomic databases

    MaxQBiQ06147.
    PaxDbiQ06147.
    PeptideAtlasiQ06147.

    Interactioni

    Protein-protein interaction databases

    BioGridi31528. 135 interactions.
    IntActiQ06147. 1 interaction.
    MINTiMINT-2784711.
    STRINGi4932.YLR260W.

    Structurei

    3D structure databases

    ProteinModelPortaliQ06147.
    SMRiQ06147. Positions 271-455, 550-667.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini266 – 405140DAGKcPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni333 – 3364Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 DAGKc domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG1597.
    GeneTreeiENSGT00690000101761.
    HOGENOMiHOG000207396.
    InParanoidiQ06147.
    KOiK04718.
    OMAiISRTSFQ.
    OrthoDBiEOG7KH9TK.

    Family and domain databases

    InterProiIPR001206. Diacylglycerol_kinase_cat_dom.
    IPR016064. NAD/diacylglycerol_kinase.
    [Graphical view]
    PfamiPF00781. DAGK_cat. 1 hit.
    [Graphical view]
    SMARTiSM00046. DAGKc. 1 hit.
    [Graphical view]
    SUPFAMiSSF111331. SSF111331. 2 hits.
    PROSITEiPS50146. DAGK. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q06147-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTLKPSKRRK GRSRHSRKKQ ITSAILTEEG IMIKAKPSSP YTYANRMADK
    60 70 80 90 100
    RSRSSIDNIS RTSFQSNISR TSFQSNSDNN SIFETASLIS CVTCLSDTDT
    110 120 130 140 150
    IDRSETSTTD TSKDDLSANP KLHYPSVNGQ LPANTVIPYG RILDARYIEK
    160 170 180 190 200
    EPLHYYDANS SPSSPLSSSM SNISEKCDLD ELESSQKKER KGNSLSRGSN
    210 220 230 240 250
    SSSSLLTSRS PFTKLVEVIF ARPRRHDVVP KRVSLYIDYK PHSSSHLKEE
    260 270 280 290 300
    DDLVEEILKR SYKNTRRNKS IFVIINPFGG KGKAKKLFMT KAKPLLLASR
    310 320 330 340 350
    CSIEVVYTKY PGHAIEIARE MDIDKYDTIA CASGDGIPHE VINGLYQRPD
    360 370 380 390 400
    HVKAFNNIAI TEIPCGSGNA MSVSCHWTNN PSYSTLCLIK SIETRIDLMC
    410 420 430 440 450
    CSQPSYAREH PKLSFLSQTY GLIAETDINT EFIRWMGPAR FELGVAFNII
    460 470 480 490 500
    QKKKYPCEIY VKYAAKSKNE LKNHYLEHKN KGSLEFQHIT MNKDNEDCDN
    510 520 530 540 550
    YNYENEYETE NEDEDEDADA DDEDSHLISR DLADSSADQI KEEDFKIKYP
    560 570 580 590 600
    LDEGIPSDWE RLDPNISNNL GIFYTGKMPY VAADTKFFPA ALPSDGTMDM
    610 620 630 640 650
    VITDARTSLT RMAPILLGLD KGSHVLQPEV LHSKILAYKI IPKLGNGLFS
    660 670 680
    VDGEKFPLEP LQVEIMPRLC KTLLRNGRYV DTDFDSM
    Length:687
    Mass (Da):77,566
    Last modified:November 1, 1996 - v1
    Checksum:i205C32F3570042FA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U17244 Genomic DNA. Translation: AAB67377.1.
    BK006945 Genomic DNA. Translation: DAA09573.1.
    PIRiS51398.
    RefSeqiNP_013361.1. NM_001182147.1.

    Genome annotation databases

    EnsemblFungiiYLR260W; YLR260W; YLR260W.
    GeneIDi850964.
    KEGGisce:YLR260W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U17244 Genomic DNA. Translation: AAB67377.1.
    BK006945 Genomic DNA. Translation: DAA09573.1.
    PIRiS51398.
    RefSeqiNP_013361.1. NM_001182147.1.

    3D structure databases

    ProteinModelPortaliQ06147.
    SMRiQ06147. Positions 271-455, 550-667.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi31528. 135 interactions.
    IntActiQ06147. 1 interaction.
    MINTiMINT-2784711.
    STRINGi4932.YLR260W.

    Proteomic databases

    MaxQBiQ06147.
    PaxDbiQ06147.
    PeptideAtlasiQ06147.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYLR260W; YLR260W; YLR260W.
    GeneIDi850964.
    KEGGisce:YLR260W.

    Organism-specific databases

    CYGDiYLR260w.
    EuPathDBiFungiDB:YLR260W.
    SGDiS000004250. LCB5.

    Phylogenomic databases

    eggNOGiCOG1597.
    GeneTreeiENSGT00690000101761.
    HOGENOMiHOG000207396.
    InParanoidiQ06147.
    KOiK04718.
    OMAiISRTSFQ.
    OrthoDBiEOG7KH9TK.

    Enzyme and pathway databases

    BioCyciMetaCyc:YLR260W-MONOMER.
    YEAST:YLR260W-MONOMER.
    ReactomeiREACT_307521. Glycosphingolipid metabolism.

    Miscellaneous databases

    NextBioi967451.
    PROiQ06147.

    Family and domain databases

    InterProiIPR001206. Diacylglycerol_kinase_cat_dom.
    IPR016064. NAD/diacylglycerol_kinase.
    [Graphical view]
    PfamiPF00781. DAGK_cat. 1 hit.
    [Graphical view]
    SMARTiSM00046. DAGKc. 1 hit.
    [Graphical view]
    SUPFAMiSSF111331. SSF111331. 2 hits.
    PROSITEiPS50146. DAGK. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
      Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
      , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
      Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "The LCB4 (YOR171c) and LCB5 (YLR260w) genes of Saccharomyces encode sphingoid long chain base kinases."
      Nagiec M.M., Skrzypek M.S., Nagiec E.E., Lester R.L., Dickson R.C.
      J. Biol. Chem. 273:19437-19442(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Accumulation of phosphorylated sphingoid long chain bases results in cell growth inhibition in Saccharomyces cerevisiae."
      Kim S., Fyrst H., Saba J.D.
      Genetics 156:1519-1529(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "Role for de novo sphingoid base biosynthesis in the heat-induced transient cell cycle arrest of Saccharomyces cerevisiae."
      Jenkins G.M., Hannun Y.A.
      J. Biol. Chem. 276:8574-8581(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "Calcium influx and signaling in yeast stimulated by intracellular sphingosine 1-phosphate accumulation."
      Birchwood C.J., Saba J.D., Dickson R.C., Cunningham K.W.
      J. Biol. Chem. 276:11712-11718(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. "Lcb4p is a key regulator of ceramide synthesis from exogenous long chain sphingoid base in Saccharomyces cerevisiae."
      Funato K., Lombardi R., Vallee B., Riezman H.
      J. Biol. Chem. 278:7325-7334(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    10. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiLCB5_YEAST
    AccessioniPrimary (citable) accession number: Q06147
    Secondary accession number(s): D6VYQ7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 31, 2006
    Last sequence update: November 1, 1996
    Last modified: June 24, 2015
    This is version 112 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 1760 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.