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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 + 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

    • 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.
    ReactomeiR-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.
    R-SCE-75105. Fatty Acyl-CoA Biosynthesis.

    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

    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)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.
    PRIDEiQ06147.

    PTM databases

    iPTMnetiQ06147.

    Interactioni

    Protein-protein interaction databases

    BioGridi31528. 135 interactors.
    IntActiQ06147. 1 interactor.
    MINTiMINT-2784711.

    Structurei

    3D structure databases

    ProteinModelPortaliQ06147.
    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

    Sequence similaritiesi

    Contains 1 DAGKc domain.PROSITE-ProRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00690000101761.
    HOGENOMiHOG000207396.
    InParanoidiQ06147.
    KOiK04718.
    OMAiENEYETE.
    OrthoDBiEOG092C1LMZ.

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi31528. 135 interactors.
    IntActiQ06147. 1 interactor.
    MINTiMINT-2784711.

    Chemistry databases

    SwissLipidsiSLP:000000110.

    PTM databases

    iPTMnetiQ06147.

    Proteomic databases

    MaxQBiQ06147.
    PRIDEiQ06147.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    EuPathDBiFungiDB:YLR260W.
    SGDiS000004250. LCB5.

    Phylogenomic databases

    GeneTreeiENSGT00690000101761.
    HOGENOMiHOG000207396.
    InParanoidiQ06147.
    KOiK04718.
    OMAiENEYETE.
    OrthoDBiEOG092C1LMZ.

    Enzyme and pathway databases

    BioCyciMetaCyc:YLR260W-MONOMER.
    YEAST:YLR260W-MONOMER.
    ReactomeiR-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.
    R-SCE-75105. Fatty Acyl-CoA Biosynthesis.

    Miscellaneous databases

    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...

    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: November 2, 2016
    This is version 125 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

    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 one 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.