Sphingoid long chain base kinase 5 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot Q06147 (LCB5_YEAST)

Last modified June 16, 2009. Version 58. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Sphingoid long chain base kinase 5
      Short name=LCB kinase 5
    EC=2.7.1.91
Alternative name(s):
    Sphinganine kinase 5

Gene names

Name:	LCB5
Ordered Locus Names:	YLR260W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	687 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	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. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6
Catalytic activity	ATP + sphinganine = ADP + sphinganine 1-phosphate. ATP + phytosphingosine = ADP + phytosphingosine 1-phosphate.
Subcellular location	Golgi apparatus membrane; Peripheral membrane protein. Ref.6
Miscellaneous	Present with 1760 molecules/cell in log phase SD medium. Ref.7
Sequence similarities	Contains 1 DAGKc domain.
Biophysicochemical properties	Kinetic parameters: K_M=2 µM for dihydrosphingosine

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Ontologies

Keywords
Biological process	Lipid metabolism Sphingolipid metabolism
Cellular component	Golgi apparatus Membrane
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Lipoprotein Palmitate Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway Inferred from electronic annotation. Source: InterPro calcium-mediated signaling Ref.5 Inferred from mutant phenotype. Source: SGD sphingolipid metabolic process Ref.2 Inferred from direct assay. Source: SGD
Cellular component	Golgi membrane Inferred from electronic annotation. Source: UniProtKB-SubCell membrane fraction Ref.2 Inferred from direct assay. Source: SGD soluble fraction Ref.2 Inferred from direct assay. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW D-erythro-sphingosine kinase activity Ref.2 Inferred from direct assay. Source: SGD diacylglycerol kinase activity Inferred from electronic annotation. Source: InterPro sphinganine kinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 687

687

Sphingoid long chain base kinase 5

PRO_0000255957

Regions

Domain

270 – 410

141

DAGKc

Amino acid modifications

Modified residue

Phosphoserine Ref.9

Modified residue

Phosphoserine Ref.8

Modified residue

168

Phosphoserine Ref.9

Modified residue

169

Phosphoserine Ref.9

Modified residue

171

Phosphoserine Ref.9

Modified residue

201

Phosphoserine Ref.9

Modified residue

202

Phosphoserine Ref.9

Modified residue

204

Phosphoserine Ref.9

Lipidation

S-palmitoyl cysteine By similarity

Lipidation

S-palmitoyl cysteine By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q06147-1 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 205C32F3570042FA
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FASTA

687

77,566

        10         20         30         40         50         60 
MTLKPSKRRK GRSRHSRKKQ ITSAILTEEG IMIKAKPSSP YTYANRMADK RSRSSIDNIS 

        70         80         90        100        110        120 
RTSFQSNISR TSFQSNSDNN SIFETASLIS CVTCLSDTDT IDRSETSTTD TSKDDLSANP 

       130        140        150        160        170        180 
KLHYPSVNGQ LPANTVIPYG RILDARYIEK EPLHYYDANS SPSSPLSSSM SNISEKCDLD 

       190        200        210        220        230        240 
ELESSQKKER KGNSLSRGSN SSSSLLTSRS PFTKLVEVIF ARPRRHDVVP KRVSLYIDYK 

       250        260        270        280        290        300 
PHSSSHLKEE DDLVEEILKR SYKNTRRNKS IFVIINPFGG KGKAKKLFMT KAKPLLLASR 

       310        320        330        340        350        360 
CSIEVVYTKY PGHAIEIARE MDIDKYDTIA CASGDGIPHE VINGLYQRPD HVKAFNNIAI 

       370        380        390        400        410        420 
TEIPCGSGNA MSVSCHWTNN PSYSTLCLIK SIETRIDLMC CSQPSYAREH PKLSFLSQTY 

       430        440        450        460        470        480 
GLIAETDINT EFIRWMGPAR FELGVAFNII QKKKYPCEIY VKYAAKSKNE LKNHYLEHKN 

       490        500        510        520        530        540 
KGSLEFQHIT MNKDNEDCDN YNYENEYETE NEDEDEDADA DDEDSHLISR DLADSSADQI 

       550        560        570        580        590        600 
KEEDFKIKYP LDEGIPSDWE RLDPNISNNL GIFYTGKMPY VAADTKFFPA ALPSDGTMDM 

       610        620        630        640        650        660 
VITDARTSLT RMAPILLGLD KGSHVLQPEV LHSKILAYKI IPKLGNGLFS VDGEKFPLEP 

       670        680 
LQVEIMPRLC KTLLRNGRYV DTDFDSM

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[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. Hoheisel J.D. Nature 387:87-90(1997) [PubMed: 9169871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	"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: 9677363] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
[3]	"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: 11102354] [Abstract] Cited for: FUNCTION.
[4]	"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: 11056159] [Abstract] Cited for: FUNCTION.
[5]	"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: 11278643] [Abstract] Cited for: FUNCTION.
[6]	"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: 12493772] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-55, MASS SPECTROMETRY.
[9]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-39; SER-168; SER-169; SER-171; SER-201; SER-202 AND SER-204, MASS SPECTROMETRY.
+	Additional computationally mapped references.

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Cross-references

Sequence databases
	U17244 Genomic DNA. Translation: AAB67377.1.
PIR	S51398.
RefSeq	NP_013361.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q06147. 3 interactions.
Proteomic databases
PeptideAtlas	Q06147.
Genome annotation databases
Ensembl	YLR260W. Saccharomyces cerevisiae. [Contig view]
GeneID	850964.
GenomeReviews	Gene locus YLR260W in contig Y13138_GR.
KEGG	sce:YLR260W.
NMPDR	fig\|4932.3.peg.4375.
Organism-specific databases
CYGD	YLR260w.
SGD	S000004250. LCB5.
Yeast-GFP	Search...
Phylogenomic databases
HOGENOM	Q06147.
OMA	Q06147. ISRTSFQ.
Enzyme and pathway databases
BRENDA	2.7.1.91. 250.
Gene expression databases
ArrayExpress	Q06147.
GermOnline	YLR260W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR001206. Diacylglycerol_kinase_cat. [Graphical view]
Pfam	PF00781. DAGK_cat. 1 hit. [Graphical view]
ProDom	PD005043. DAGKc. 1 hit. [Graphical view] [Entries sharing at least one domain]
SMART	SM00046. DAGKc. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	967451.

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Entry information

Entry name

LCB5_YEAST

Accession

Primary (citable) accession number: Q06147

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 31, 2006
Last sequence update:	November 1, 1996
Last modified:	June 16, 2009
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents