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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: -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

Miscellaneous

Present with 1760 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

ATP + a sphingoid base = ADP + a sphingoid base 1-phosphate.1 Publication

Kineticsi

  1. KM=2 µM for dihydrosphingosine1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei308ATPPROSITE-ProRule annotation1
    Active sitei335Proton donor/acceptorBy similarity1
    Binding sitei340ATPPROSITE-ProRule annotation1
    Binding sitei434ATPPROSITE-ProRule annotation1
    Binding sitei440ATPPROSITE-ProRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi276 – 278ATPPROSITE-ProRule annotation3
    Nucleotide bindingi366 – 368ATPPROSITE-ProRule annotation3
    Nucleotide bindingi652 – 654ATPPROSITE-ProRule annotation3

    GO - Molecular functioni

    GO - Biological processi

    • calcium-mediated signaling Source: SGD
    • response to heat Source: SGD
    • sphingolipid metabolic process Source: SGD

    Keywordsi

    Molecular functionKinase, Transferase
    Biological processLipid metabolism, Sphingolipid metabolism
    LigandATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:YLR260W-MONOMER
    YEAST:YLR260W-MONOMER
    ReactomeiR-SCE-1483206 Glycerophospholipid biosynthesis
    R-SCE-1660661 Sphingolipid de novo biosynthesis
    R-SCE-1660662 Glycosphingolipid metabolism
    R-SCE-390471 Association of TriC/CCT with target proteins during biosynthesis
    R-SCE-5218921 VEGFR2 mediated cell proliferation

    Chemistry databases

    SwissLipidsiSLP:000000110

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sphingoid long chain base kinase 5 (EC:2.7.1.911 Publication)
    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
    Proteomesi
    • UP000002311 Componenti: Chromosome XII

    Organism-specific databases

    EuPathDBiFungiDB:YLR260W
    SGDiS000004250 LCB5

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Golgi apparatus, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002559571 – 687Sphingoid long chain base kinase 5Add BLAST687

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Lipidationi91S-palmitoyl cysteineBy similarity1
    Lipidationi94S-palmitoyl cysteineBy similarity1

    Keywords - PTMi

    Lipoprotein, Palmitate

    Proteomic databases

    MaxQBiQ06147
    PaxDbiQ06147
    PRIDEiQ06147

    PTM databases

    iPTMnetiQ06147

    Interactioni

    Protein-protein interaction databases

    BioGridi31528, 165 interactors
    IntActiQ06147, 1 interactor
    MINTiQ06147
    STRINGi4932.YLR260W

    Structurei

    3D structure databases

    ProteinModelPortaliQ06147
    SMRiQ06147
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini266 – 405DAGKcPROSITE-ProRule annotationAdd BLAST140

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni333 – 336Substrate bindingBy similarity4

    Phylogenomic databases

    GeneTreeiENSGT00690000101761
    HOGENOMiHOG000207396
    InParanoidiQ06147
    KOiK04718
    OMAiMEPEHAK
    OrthoDBiEOG092C1LMZ

    Family and domain databases

    Gene3Di3.40.50.10330, 1 hit
    InterProiView protein in InterPro
    IPR017438 ATP-NAD_kinase_N
    IPR001206 Diacylglycerol_kinase_cat_dom
    IPR016064 NAD/diacylglycerol_kinase_sf
    PfamiView protein in Pfam
    PF00781 DAGK_cat, 1 hit
    SMARTiView protein in SMART
    SM00046 DAGKc, 1 hit
    SUPFAMiSSF111331 SSF111331, 2 hits
    PROSITEiView protein in PROSITE
    PS50146 DAGK, 1 hit

    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

    Similar proteinsi

    Entry informationi

    Entry nameiLCB5_YEAST
    AccessioniPrimary (citable) accession number: Q06147
    Secondary accession number(s): D6VYQ7
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 31, 2006
    Last sequence update: November 1, 1996
    Last modified: May 23, 2018
    This is version 138 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

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