Sphingoid long chain base kinase 5 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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Q06147 (LCB5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 92. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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 (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	687 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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

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 Reference proteome
Gene Ontology (GO)
Biological_process	calcium-mediated signaling Inferred from mutant phenotype Ref.6. Source: SGD protein kinase C-activating G-protein coupled receptor signaling pathway Inferred from electronic annotation. Source: InterPro response to heat Inferred from direct assay PubMed 11967828. Source: SGD sphingolipid metabolic process Inferred from direct assay Ref.3. Source: SGD
Cellular_component	Golgi apparatus Inferred from direct assay Ref.7. Source: SGD Golgi membrane Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from direct assay Ref.7. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW D-erythro-sphingosine kinase activity Inferred from direct assay Ref.3. Source: SGD diacylglycerol kinase activity Inferred from electronic annotation. Source: InterPro sphinganine kinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

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

266 – 405

140

DAGKc

Amino acid modifications

Modified residue

Phosphoserine Ref.10

Modified residue

Phosphoserine Ref.9

Modified residue

168

Phosphoserine Ref.10

Modified residue

169

Phosphoserine Ref.10

Modified residue

171

Phosphoserine Ref.10

Modified residue

201

Phosphoserine Ref.10

Modified residue

202

Phosphoserine Ref.10

Modified residue

204

Phosphoserine Ref.10

Lipidation

S-palmitoyl cysteine By similarity

Lipidation

S-palmitoyl cysteine By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q06147 [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

« Hide

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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-55, MASS SPECTROMETRY.
[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: 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U17244 Genomic DNA. Translation: AAB67377.1. BK006945 Genomic DNA. Translation: DAA09573.1.
PIR	S51398.
RefSeq	NP_013361.1. NM_001182147.1.
3D structure databases
ProteinModelPortal	Q06147.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q06147. 1 interaction.
MINT	MINT-2784711.
STRING	4932.YLR260W.
Proteomic databases
PaxDb	Q06147.
PeptideAtlas	Q06147.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YLR260W; YLR260W; YLR260W.
GeneID	850964.
KEGG	sce:YLR260W.
Organism-specific databases
CYGD	YLR260w.
SGD	S000004250. LCB5.
Phylogenomic databases
eggNOG	COG1597.
GeneTree	ENSGT00690000101761.
HOGENOM	HOG000207396.
KO	K04718.
OMA	ISRTSFQ.
OrthoDB	EOG4H75M6.
Enzyme and pathway databases
BioCyc	MetaCyc:YLR260W-MONOMER.
Gene expression databases
Genevestigator	Q06147.
GermOnline	YLR260W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR001206. Diacylglycerol_kinase_cat_dom. [Graphical view]
Pfam	PF00781. DAGK_cat. 1 hit. [Graphical view]
SMART	SM00046. DAGKc. 1 hit. [Graphical view]
PROSITE	PS50146. DAGK. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	967451.

Entry information

Entry name

LCB5_YEAST

Accession

Primary (citable) accession number: Q06147
Secondary accession number(s): D6VYQ7

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 31, 2006
Last sequence update:	November 1, 1996
Last modified:	April 3, 2013
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XII

Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents