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Q06147

- LCB5_YEAST

UniProt

Q06147 - LCB5_YEAST

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Protein
Sphingoid long chain base kinase 5
Gene
LCB5, YLR260W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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 – 3081ATP By similarity
Active sitei335 – 3351Proton donor/acceptor By similarity
Binding sitei340 – 3401ATP By similarity
Binding sitei434 – 4341ATP By similarity
Binding sitei440 – 4401ATP By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi276 – 2783ATP By similarity
Nucleotide bindingi366 – 3683ATP By similarity
Nucleotide bindingi652 – 6543ATP By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. D-erythro-sphingosine kinase activity Source: SGD
  3. NAD+ kinase activity Source: InterPro
  4. diacylglycerol kinase activity Source: InterPro
  5. sphinganine kinase activity Source: UniProtKB-EC
Complete GO annotation...

GO - Biological processi

  1. calcium-mediated signaling Source: SGD
  2. protein kinase C-activating G-protein coupled receptor signaling pathway Source: InterPro
  3. response to heat Source: SGD
  4. 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_188975. 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: Chromosome XII

Organism-specific databases

CYGDiYLR260w.
SGDiS000004250. LCB5.

Subcellular locationi

Golgi apparatus membrane; Peripheral membrane protein 1 Publication

GO - Cellular componenti

  1. Golgi apparatus Source: SGD
  2. Golgi membrane Source: UniProtKB-SubCell
  3. 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 5
PRO_0000255957Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Lipoprotein, Palmitate

Proteomic databases

MaxQBiQ06147.
PaxDbiQ06147.
PeptideAtlasiQ06147.

Expressioni

Gene expression databases

GenevestigatoriQ06147.

Interactioni

Protein-protein interaction databases

BioGridi31528. 134 interactions.
IntActiQ06147. 1 interaction.
MINTiMINT-2784711.
STRINGi4932.YLR260W.

Structurei

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini266 – 405140DAGKc
Add
BLAST

Region

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

Sequence similaritiesi

Contains 1 DAGKc domain.

Phylogenomic databases

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

Family and domain databases

InterProiIPR016064. ATP-NAD_kinase_PpnK-typ.
IPR001206. Diacylglycerol_kinase_cat_dom.
[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

MTLKPSKRRK GRSRHSRKKQ ITSAILTEEG IMIKAKPSSP YTYANRMADK    50
RSRSSIDNIS RTSFQSNISR TSFQSNSDNN SIFETASLIS CVTCLSDTDT 100
IDRSETSTTD TSKDDLSANP KLHYPSVNGQ LPANTVIPYG RILDARYIEK 150
EPLHYYDANS SPSSPLSSSM SNISEKCDLD ELESSQKKER KGNSLSRGSN 200
SSSSLLTSRS PFTKLVEVIF ARPRRHDVVP KRVSLYIDYK PHSSSHLKEE 250
DDLVEEILKR SYKNTRRNKS IFVIINPFGG KGKAKKLFMT KAKPLLLASR 300
CSIEVVYTKY PGHAIEIARE MDIDKYDTIA CASGDGIPHE VINGLYQRPD 350
HVKAFNNIAI TEIPCGSGNA MSVSCHWTNN PSYSTLCLIK SIETRIDLMC 400
CSQPSYAREH PKLSFLSQTY GLIAETDINT EFIRWMGPAR FELGVAFNII 450
QKKKYPCEIY VKYAAKSKNE LKNHYLEHKN KGSLEFQHIT MNKDNEDCDN 500
YNYENEYETE NEDEDEDADA DDEDSHLISR DLADSSADQI KEEDFKIKYP 550
LDEGIPSDWE RLDPNISNNL GIFYTGKMPY VAADTKFFPA ALPSDGTMDM 600
VITDARTSLT RMAPILLGLD KGSHVLQPEV LHSKILAYKI IPKLGNGLFS 650
VDGEKFPLEP LQVEIMPRLC KTLLRNGRYV DTDFDSM 687
Length:687
Mass (Da):77,566
Last modified:November 1, 1996 - v1
Checksum:i205C32F3570042FA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
U17244 Genomic DNA. Translation: AAB67377.1 .
BK006945 Genomic DNA. Translation: DAA09573.1 .
PIRi S51398.
RefSeqi NP_013361.1. NM_001182147.1.

3D structure databases

ProteinModelPortali Q06147.
SMRi Q06147. Positions 271-455, 550-667.
ModBasei Search...

Protein-protein interaction databases

BioGridi 31528. 134 interactions.
IntActi Q06147. 1 interaction.
MINTi MINT-2784711.
STRINGi 4932.YLR260W.

Proteomic databases

MaxQBi Q06147.
PaxDbi Q06147.
PeptideAtlasi Q06147.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YLR260W ; YLR260W ; YLR260W .
GeneIDi 850964.
KEGGi sce:YLR260W.

Organism-specific databases

CYGDi YLR260w.
SGDi S000004250. LCB5.

Phylogenomic databases

eggNOGi COG1597.
GeneTreei ENSGT00690000101761.
HOGENOMi HOG000207396.
KOi K04718.
OMAi ISRTSFQ.
OrthoDBi EOG7KH9TK.

Enzyme and pathway databases

BioCyci MetaCyc:YLR260W-MONOMER.
YEAST:YLR260W-MONOMER.
Reactomei REACT_188975. Glycosphingolipid metabolism.

Miscellaneous databases

NextBioi 967451.

Gene expression databases

Genevestigatori Q06147.

Family and domain databases

InterProi IPR016064. ATP-NAD_kinase_PpnK-typ.
IPR001206. Diacylglycerol_kinase_cat_dom.
[Graphical view ]
Pfami PF00781. DAGK_cat. 1 hit.
[Graphical view ]
SMARTi SM00046. DAGKc. 1 hit.
[Graphical view ]
SUPFAMi SSF111331. SSF111331. 2 hits.
PROSITEi PS50146. DAGK. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 104 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.

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

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