Dihydrosphingosine 1-phosphate phosphatase LCB3 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Contribute

Send feedback

Read comments (?) or add your own

P47013 (DS1P1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 99. History...

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

Documents (3) |

Third-party data

text xml rdf/xml gff fasta

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

Names and origin

Protein names

Recommended name:
Dihydrosphingosine 1-phosphate phosphatase LCB3
EC=3.1.3.-

Alternative name(s):
Long-chain base protein 3
Sphingolipid resistance protein 2

Gene names

Name:	LCB3
Synonyms:	LBP1, YSR2
Ordered Locus Names:	YJL134W
ORF Names:	J0671

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	409 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Dihydrosphingosine 1-phosphate phosphatase required for efficient ceramide synthesis from exogenous sphingoid bases. Involved in endocytosis and calcium-mediated signaling. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14
Subcellular location	Endoplasmic reticulum membrane; Multi-pass membrane protein Ref.5 Ref.7 Ref.9.
Post-translational modification	Glycosylated. Ref.13
Sequence similarities	Belongs to the type 2 lipid phosphate phosphatase family.

Ontologies

Keywords
Biological process	Lipid metabolism Sphingolipid metabolism
Cellular component	Endoplasmic reticulum Membrane
Domain	Transmembrane Transmembrane helix
Molecular function	Hydrolase
PTM	Glycoprotein Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	calcium-mediated signaling Inferred from mutant phenotype Ref.10. Source: SGD sphingolipid biosynthetic process Traceable author statement Ref.9. Source: SGD
Cellular_component	endoplasmic reticulum Inferred from direct assay Ref.7. Source: SGD endoplasmic reticulum membrane Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from sequence model PubMed 12192589. Source: SGD
Molecular_function	sphingosine-1-phosphate phosphatase activity Inferred from direct assay Ref.5. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 409

409

Dihydrosphingosine 1-phosphate phosphatase LCB3

PRO_0000203037

Regions

Topological domain

1 – 86

Lumenal Ref.13 Ref.16

Transmembrane

87 – 107

Helical; Name=1

Topological domain

108 – 112

Cytoplasmic Ref.13 Ref.16

Transmembrane

113 – 133

Helical; Name=2

Topological domain

134 – 182

Lumenal Ref.13 Ref.16

Transmembrane

183 – 203

Helical; Name=3

Topological domain

204 – 207

Cytoplasmic Ref.13 Ref.16

Transmembrane

208 – 228

Helical; Name=4

Topological domain

229 – 245

Lumenal Ref.13 Ref.16

Transmembrane

246 – 266

Helical; Name=5

Topological domain

267 – 276

Cytoplasmic Ref.13 Ref.16

Transmembrane

277 – 297

Helical; Name=6

Topological domain

298 – 315

Lumenal Ref.13 Ref.16

Transmembrane

316 – 336

Helical; Name=7

Topological domain

337 – 384

Cytoplasmic Ref.13 Ref.16

Transmembrane

385 – 405

Helical; Name=8

Topological domain

406 – 409

Lumenal Ref.13 Ref.16

Amino acid modifications

Modified residue

Phosphothreonine Ref.17

Modified residue

Phosphoserine Ref.15 Ref.17 Ref.18 Ref.19

Experimental info

Mutagenesis

128

K → A: Impairs dihydrosphingosine 1-phosphate phosphatase activity. Ref.13

Mutagenesis

160

H → A: Impairs dihydrosphingosine 1-phosphate phosphatase activity. Ref.13

Mutagenesis

210

H → A: Impairs dihydrosphingosine 1-phosphate phosphatase activity. Ref.13

Sequences

Sequence

Length

Mass (Da)

Tools

P47013 [UniParc].

Last modified February 1, 1996. Version 1.
Checksum: E0CD7D0F169447C3
Show »

FASTA

409

47,372

        10         20         30         40         50         60 
MVDGLNTSNI RKRARTLSNP NDFQEPNYLL DPGNHPSDHF RTRMSKFRFN IREKLLVFTN 

        70         80         90        100        110        120 
NQSFTLSRWQ KKYRSAFNDL YFTYTSLMGS HTFYVLCLPM PVWFGYFETT KDMVYILGYS 

       130        140        150        160        170        180 
IYLSGFFKDY WCLPRPRAPP LHRITLSEYT TKEYGAPSSH TANATGVSLL FLYNIWRMQE 

       190        200        210        220        230        240 
SSVMVQLLLS CVVLFYYMTL VFGRIYCGMH GILDLVSGGL IGIVCFIVRM YFKYRFPGLR 

       250        260        270        280        290        300 
IEEHWWFPLF SVGWGLLLLF KHVKPVDECP CFQDSVAFMG VVSGIECCDW LGKVFGVTLV 

       310        320        330        340        350        360 
YNLEPNCGWR LTLARLLVGL PCVVIWKYVI SKPMIYTLLI KVFHLKDDRN VAARKRLEAT 

       370        380        390        400 
HKEGASKYEC PLYIGEPKID ILGRFIIYAG VPFTVVMCSP VLFSLLNIA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence analysis of a 40.7 kb segment from the left arm of yeast chromosome X reveals 14 known genes and 13 new open reading frames including homologues of genes clustered on the right arm of chromosome XI." Katsoulou C., Tzermia M., Tavernarakis N., Alexandraki D. Yeast 12:787-797(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X." Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K. Karpfinger-Hartl L. EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Identification of a Saccharomyces gene, LCB3, necessary for incorporation of exogenous long chain bases into sphingolipids." Qie L., Nagiec M.M., Baltisberger J.A., Lester R.L., Dickson R.C. J. Biol. Chem. 272:16110-16117(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"Identification and characterization of Saccharomyces cerevisiae dihydrosphingosine-1-phosphate phosphatase." Mao C., Wadleigh M., Jenkins G.M., Hannun Y.A., Obeid L.M. J. Biol. Chem. 272:28690-28694(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[6]	"Sphingoid base 1-phosphate phosphatase: a key regulator of sphingolipid metabolism and stress response." Mandala S.M., Thornton R., Tu Z., Kurtz M.B., Nickels J., Broach J., Menzeleev R., Spiegel S. Proc. Natl. Acad. Sci. U.S.A. 95:150-155(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"The dihydrosphingosine-1-phosphate phosphatases of Saccharomyces cerevisiae are important regulators of cell proliferation and heat stress responses." Mao C., Saba J.D., Obeid L.M. Biochem. J. 342:667-675(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[8]	"Sphingoid base synthesis requirement for endocytosis in Saccharomyces cerevisiae." Zanolari B., Friant S., Funato K., Suetterlin C., Stevenson B.J., Riezman H. EMBO J. 19:2824-2833(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Yeast sphingosine-1-phosphate phosphatases: assay, expression, deletion, purification, and cellular localization by GFP tagging." Mao C., Obeid L.M. Methods Enzymol. 311:223-232(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[10]	"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.
[11]	"Mutant analysis reveals complex regulation of sphingolipid long chain base phosphates and long chain bases during heat stress in yeast." Ferguson-Yankey S.R., Skrzypek M.S., Lester R.L., Dickson R.C. Yeast 19:573-586(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[12]	"Ceramide/long-chain base phosphate rheostat in Saccharomyces cerevisiae: regulation of ceramide synthesis by Elo3p and Cka2p." Kobayashi S.D., Nagiec M.M. Eukaryot. Cell 2:284-294(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"Transmembrane topology of sphingoid long-chain base-1-phosphate phosphatase, Lcb3p." Kihara A., Sano T., Iwaki S., Igarashi Y. Genes Cells 8:525-535(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF LYS-128; HIS-160 AND HIS-210, GLYCOSYLATION, TOPOLOGY.
[14]	"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.
[15]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-18, MASS SPECTROMETRY. Strain: YAL6B.
[16]	"A global topology map of the Saccharomyces cerevisiae membrane proteome." Kim H., Melen K., Oesterberg M., von Heijne G. Proc. Natl. Acad. Sci. U.S.A. 103:11142-11147(2006) [PubMed] [Europe PMC] [Abstract] Cited for: TOPOLOGY [LARGE SCALE ANALYSIS]. Strain: ATCC 208353 / W303-1A.
[17]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16 AND SER-18, MASS SPECTROMETRY. Strain: ADR376.
[18]	"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-18, MASS SPECTROMETRY.
[19]	"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-18, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X87371 Genomic DNA. Translation: CAA60821.1. Z49410 Genomic DNA. Translation: CAA89430.1. BK006943 Genomic DNA. Translation: DAA08666.1.
PIR	S55178.
RefSeq	NP_012401.1. NM_001181567.1.
3D structure databases
ProteinModelPortal	P47013.
SMR	P47013. Positions 108-231.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5685N.
IntAct	P47013. 3 interactions.
MINT	MINT-572017.
STRING	4932.YJL134W.
Proteomic databases
PaxDb	P47013.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YJL134W; YJL134W; YJL134W.
GeneID	853307.
KEGG	sce:YJL134W.
Organism-specific databases
CYGD	YJL134w.
SGD	S000003670. LCB3.
Phylogenomic databases
eggNOG	COG0671.
GeneTree	ENSGT00390000017322.
HOGENOM	HOG000066080.
KO	K04716.
OMA	YHTAFNG.
OrthoDB	EOG44F9K4.
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER3O-419.
Gene expression databases
Genevestigator	P47013.
GermOnline	YJL134W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	1.20.144.10. 1 hit.
InterPro	IPR016118. P_Acid_Pase/Cl_peroxidase_N. IPR000326. P_Acid_Pase_2/haloperoxidase. [Graphical view]
Pfam	PF01569. PAP2. 1 hit. [Graphical view]
SMART	SM00014. acidPPc. 1 hit. [Graphical view]
SUPFAM	SSF48317. AcPase_VanPerase. 1 hit.
ProtoNet	Search...
Other
NextBio	973636.

Entry information

Entry name

DS1P1_YEAST

Accession

Primary (citable) accession number: P47013
Secondary accession number(s): D6VW50

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	February 1, 1996
Last modified:	May 1, 2013
This is version 99 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 X

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

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

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