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Protein

Sphingoid long chain base kinase 4

Gene

LCB4

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 (PubMed:9677363, PubMed:11102354, PubMed:11795842, PubMed:16141212). Involved in the biosynthesis of sphingolipids and ceramides (PubMed:12493772). Required with LCB3 for an effective incorporation of DHS into ceramides through a phosphorylation-dephosphorylation cycle. Involved in heat-induced transient cell cycle arrest (PubMed:11056159). Accumulation of phosphorylated sphingoid long chain bases (LCBPs) stimulates calcium influx and activates calcineurin signaling (PubMed:11278643). Involved in heat-stress resistance (PubMed:11967828).8 Publications

Catalytic activityi

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

Kineticsi

  1. KM=7.7 µM for sphinganine1 Publication
  2. KM=25 µM for ATP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei266ATPPROSITE-ProRule annotation1
    Active sitei293Proton donor/acceptorBy similarity1
    Binding sitei298ATPPROSITE-ProRule annotation1
    Binding sitei392ATPPROSITE-ProRule annotation1
    Binding sitei398ATPPROSITE-ProRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi234 – 236ATPPROSITE-ProRule annotation3
    Nucleotide bindingi324 – 326ATPPROSITE-ProRule annotation3
    Nucleotide bindingi589 – 591ATPPROSITE-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
    • 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:YOR171C-MONOMER.
    YEAST:YOR171C-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:000000109.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sphingoid long chain base kinase 41 Publication (EC:2.7.1.911 Publication)
    Short name:
    LCB kinase 41 Publication
    Alternative name(s):
    Sphinganine kinase 4Curated
    Gene namesi
    Name:LCB41 Publication
    Ordered Locus Names:YOR171CImported
    ORF Names:O3615
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XV

    Organism-specific databases

    EuPathDBiFungiDB:YOR171C.
    SGDiS000005697. LCB4.

    Subcellular locationi

    GO - Cellular componenti

    • cortical endoplasmic reticulum Source: SGD
    • endoplasmic reticulum Source: SGD
    • endoplasmic reticulum membrane Source: UniProtKB-SubCell
    • Golgi apparatus Source: SGD
    • Golgi membrane Source: UniProtKB-SubCell
    • late endosome membrane Source: UniProtKB-SubCell
    • plasma membrane Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Cell membrane, Endoplasmic reticulum, Endosome, Golgi apparatus, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002559561 – 624Sphingoid long chain base kinase 4Add BLAST624

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Lipidationi43S-palmitoyl cysteine1 Publication1
    Lipidationi46S-palmitoyl cysteine1 Publication1
    Modified residuei111PhosphoserineCombined sources1
    Modified residuei120PhosphoserineCombined sources1
    Cross-linki148Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei154PhosphoserineCombined sources1
    Modified residuei160PhosphoserineCombined sources1
    Modified residuei451Phosphoserine; by PHO85Combined sources1 Publication1
    Modified residuei454PhosphoserineCombined sources1
    Modified residuei455Phosphoserine; by PHO85Combined sources1 Publication1
    Modified residuei460PhosphoserineCombined sources1

    Post-translational modificationi

    Phosphorylated by the cyclin-CDKs PCL1-PHO85 and PCL2-PHO85. Phosphorylation is a prerequisite to ubiquitination. The phosphorylation level depends on sterol composition and may also be involved in subcellular location (PubMed:16141212).2 Publications
    Ubiquitinated. The ubiquitination leads to degradation in the vacuole.1 Publication

    Keywords - PTMi

    Isopeptide bond, Lipoprotein, Palmitate, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiQ12246.
    PRIDEiQ12246.

    PTM databases

    iPTMnetiQ12246.
    SwissPalmiQ12246.

    Interactioni

    Protein-protein interaction databases

    BioGridi34565. 104 interactors.
    DIPiDIP-2844N.
    IntActiQ12246. 4 interactors.
    MINTiMINT-502657.

    Structurei

    3D structure databases

    ProteinModelPortaliQ12246.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini224 – 363DAGKcPROSITE-ProRule annotationAdd BLAST140

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni291 – 294Substrate bindingBy similarity4

    Sequence similaritiesi

    Contains 1 DAGKc domain.PROSITE-ProRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00690000101761.
    HOGENOMiHOG000207396.
    InParanoidiQ12246.
    KOiK04718.
    OMAiRWAHAIS.
    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.

    Q12246-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVVQKKLRAI LTDEGVLIKS QSHHMFNKHG QLRSGDSLSL LSCLSCLDDG
    60 70 80 90 100
    TLSSDGGSFD EDDSLELLPL NTTIPFNRIL NAKYVNVGQK GFNNGKISSN
    110 120 130 140 150
    PFQTENLSSS SENDDVENHS LSNDKAPVSE SQSFPKKDKW DTKTNTVKVS
    160 170 180 190 200
    PDDSQDNSPS LGIKDNQQLI ELTFAVPKGH DVIPQKLTLL IDHVSRKSRA
    210 220 230 240 250
    NTGEENISSG TVEEILEKSY ENSKRNRSIL VIINPHGGKG TAKNLFLTKA
    260 270 280 290 300
    RPILVESGCK IEIAYTKYAR HAIDIAKDLD ISKYDTIACA SGDGIPYEVI
    310 320 330 340 350
    NGLYRRPDRV DAFNKLAVTQ LPCGSGNAMS ISCHWTNNPS YAALCLVKSI
    360 370 380 390 400
    ETRIDLMCCS QPSYMNEWPR LSFLSQTYGV IAESDINTEF IRWMGPVRFN
    410 420 430 440 450
    LGVAFNIIQG KKYPCEVFVK YAAKSKKELK VHFLENKDKN KGCLTFEPNP
    460 470 480 490 500
    SPNSSPDLLS KNNINNSTKD ELSPNFLNED NFKLKYPMTE PVPRDWEKMD
    510 520 530 540 550
    SELTDNLTIF YTGKMPYIAK DTKFFPAALP ADGTIDLVIT DARIPVTRMT
    560 570 580 590 600
    PILLSLDKGS HVLEPEVIHS KILAYKIIPK VESGLFSVDG EKFPLEPLQV
    610 620
    EIMPMLCKTL LRNGRYIDTE FESM
    Length:624
    Mass (Da):69,639
    Last modified:November 1, 1996 - v1
    Checksum:iE033A3BAC604D4BB
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U55021 Genomic DNA. Translation: AAB47416.1.
    Z75078 Genomic DNA. Translation: CAA99378.1.
    BK006948 Genomic DNA. Translation: DAA10943.1.
    PIRiS67059.
    RefSeqiNP_014814.1. NM_001183590.1.

    Genome annotation databases

    EnsemblFungiiYOR171C; YOR171C; YOR171C.
    GeneIDi854342.
    KEGGisce:YOR171C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U55021 Genomic DNA. Translation: AAB47416.1.
    Z75078 Genomic DNA. Translation: CAA99378.1.
    BK006948 Genomic DNA. Translation: DAA10943.1.
    PIRiS67059.
    RefSeqiNP_014814.1. NM_001183590.1.

    3D structure databases

    ProteinModelPortaliQ12246.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi34565. 104 interactors.
    DIPiDIP-2844N.
    IntActiQ12246. 4 interactors.
    MINTiMINT-502657.

    Chemistry databases

    SwissLipidsiSLP:000000109.

    PTM databases

    iPTMnetiQ12246.
    SwissPalmiQ12246.

    Proteomic databases

    MaxQBiQ12246.
    PRIDEiQ12246.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYOR171C; YOR171C; YOR171C.
    GeneIDi854342.
    KEGGisce:YOR171C.

    Organism-specific databases

    EuPathDBiFungiDB:YOR171C.
    SGDiS000005697. LCB4.

    Phylogenomic databases

    GeneTreeiENSGT00690000101761.
    HOGENOMiHOG000207396.
    InParanoidiQ12246.
    KOiK04718.
    OMAiRWAHAIS.
    OrthoDBiEOG092C1LMZ.

    Enzyme and pathway databases

    BioCyciMetaCyc:YOR171C-MONOMER.
    YEAST:YOR171C-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

    PROiQ12246.

    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 nameiLCB4_YEAST
    AccessioniPrimary (citable) accession number: Q12246
    Secondary accession number(s): D6W2M7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 31, 2006
    Last sequence update: November 1, 1996
    Last modified: November 2, 2016
    This is version 134 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 2840 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 XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: 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.