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Protein

Dihydrosphingosine 1-phosphate phosphatase LCB3

Gene

LCB3

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

Dihydrosphingosine 1-phosphate phosphatase required for efficient ceramide synthesis from exogenous sphingoid bases. Involved in endocytosis and calcium-mediated signaling.11 Publications

GO - Molecular functioni

  1. sphingosine-1-phosphate phosphatase activity Source: SGD

GO - Biological processi

  1. calcium-mediated signaling Source: SGD
  2. dephosphorylation Source: GOC
  3. sphingolipid biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER3O-419.
YEAST:MONOMER3O-419.
ReactomeiREACT_285133. Sphingolipid de novo biosynthesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydrosphingosine 1-phosphate phosphatase LCB3 (EC:3.1.3.-)
Alternative name(s):
Long-chain base protein 3
Sphingolipid resistance protein 2
Gene namesi
Name:LCB3
Synonyms:LBP1, YSR2
Ordered Locus Names:YJL134W
ORF Names:J0671
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome X

Organism-specific databases

CYGDiYJL134w.
EuPathDBiFungiDB:YJL134W.
SGDiS000003670. LCB3.

Subcellular locationi

  1. Endoplasmic reticulum membrane 3 Publications; Multi-pass membrane protein 3 Publications

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 8686LumenalAdd
BLAST
Transmembranei87 – 10721Helical; Name=1Add
BLAST
Topological domaini108 – 1125Cytoplasmic
Transmembranei113 – 13321Helical; Name=2Add
BLAST
Topological domaini134 – 18249LumenalAdd
BLAST
Transmembranei183 – 20321Helical; Name=3Add
BLAST
Topological domaini204 – 2074Cytoplasmic
Transmembranei208 – 22821Helical; Name=4Add
BLAST
Topological domaini229 – 24517LumenalAdd
BLAST
Transmembranei246 – 26621Helical; Name=5Add
BLAST
Topological domaini267 – 27610Cytoplasmic
Transmembranei277 – 29721Helical; Name=6Add
BLAST
Topological domaini298 – 31518LumenalAdd
BLAST
Transmembranei316 – 33621Helical; Name=7Add
BLAST
Topological domaini337 – 38448CytoplasmicAdd
BLAST
Transmembranei385 – 40521Helical; Name=8Add
BLAST
Topological domaini406 – 4094Lumenal

GO - Cellular componenti

  1. endoplasmic reticulum Source: SGD
  2. endoplasmic reticulum membrane Source: UniProtKB-SubCell
  3. integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi128 – 1281K → A: Impairs dihydrosphingosine 1-phosphate phosphatase activity. 1 Publication
Mutagenesisi160 – 1601H → A: Impairs dihydrosphingosine 1-phosphate phosphatase activity. 1 Publication
Mutagenesisi210 – 2101H → A: Impairs dihydrosphingosine 1-phosphate phosphatase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 409409Dihydrosphingosine 1-phosphate phosphatase LCB3PRO_0000203037Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei16 – 161Phosphothreonine2 Publications
Modified residuei18 – 181Phosphoserine2 Publications

Post-translational modificationi

Glycosylated.1 Publication

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

MaxQBiP47013.
PaxDbiP47013.

Expressioni

Gene expression databases

GenevestigatoriP47013.

Interactioni

Protein-protein interaction databases

BioGridi33622. 77 interactions.
DIPiDIP-5685N.
IntActiP47013. 4 interactions.
MINTiMINT-572017.
STRINGi4932.YJL134W.

Structurei

3D structure databases

ProteinModelPortaliP47013.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0671.
GeneTreeiENSGT00390000017322.
HOGENOMiHOG000066080.
InParanoidiP47013.
KOiK04716.
OMAiLMGSHTF.
OrthoDBiEOG7F519P.

Family and domain databases

Gene3Di1.20.144.10. 1 hit.
InterProiIPR000326. P_Acid_Pase_2/haloperoxidase.
[Graphical view]
PfamiPF01569. PAP2. 1 hit.
[Graphical view]
SMARTiSM00014. acidPPc. 1 hit.
[Graphical view]
SUPFAMiSSF48317. SSF48317. 1 hit.

Sequencei

Sequence statusi: Complete.

P47013-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDGLNTSNI RKRARTLSNP NDFQEPNYLL DPGNHPSDHF RTRMSKFRFN
60 70 80 90 100
IREKLLVFTN NQSFTLSRWQ KKYRSAFNDL YFTYTSLMGS HTFYVLCLPM
110 120 130 140 150
PVWFGYFETT KDMVYILGYS IYLSGFFKDY WCLPRPRAPP LHRITLSEYT
160 170 180 190 200
TKEYGAPSSH TANATGVSLL FLYNIWRMQE SSVMVQLLLS CVVLFYYMTL
210 220 230 240 250
VFGRIYCGMH GILDLVSGGL IGIVCFIVRM YFKYRFPGLR IEEHWWFPLF
260 270 280 290 300
SVGWGLLLLF KHVKPVDECP CFQDSVAFMG VVSGIECCDW LGKVFGVTLV
310 320 330 340 350
YNLEPNCGWR LTLARLLVGL PCVVIWKYVI SKPMIYTLLI KVFHLKDDRN
360 370 380 390 400
VAARKRLEAT HKEGASKYEC PLYIGEPKID ILGRFIIYAG VPFTVVMCSP

VLFSLLNIA
Length:409
Mass (Da):47,372
Last modified:February 1, 1996 - v1
Checksum:iE0CD7D0F169447C3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X87371 Genomic DNA. Translation: CAA60821.1.
Z49410 Genomic DNA. Translation: CAA89430.1.
BK006943 Genomic DNA. Translation: DAA08666.1.
PIRiS55178.
RefSeqiNP_012401.1. NM_001181567.1.

Genome annotation databases

EnsemblFungiiYJL134W; YJL134W; YJL134W.
GeneIDi853307.
KEGGisce:YJL134W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X87371 Genomic DNA. Translation: CAA60821.1.
Z49410 Genomic DNA. Translation: CAA89430.1.
BK006943 Genomic DNA. Translation: DAA08666.1.
PIRiS55178.
RefSeqiNP_012401.1. NM_001181567.1.

3D structure databases

ProteinModelPortaliP47013.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33622. 77 interactions.
DIPiDIP-5685N.
IntActiP47013. 4 interactions.
MINTiMINT-572017.
STRINGi4932.YJL134W.

Proteomic databases

MaxQBiP47013.
PaxDbiP47013.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJL134W; YJL134W; YJL134W.
GeneIDi853307.
KEGGisce:YJL134W.

Organism-specific databases

CYGDiYJL134w.
EuPathDBiFungiDB:YJL134W.
SGDiS000003670. LCB3.

Phylogenomic databases

eggNOGiCOG0671.
GeneTreeiENSGT00390000017322.
HOGENOMiHOG000066080.
InParanoidiP47013.
KOiK04716.
OMAiLMGSHTF.
OrthoDBiEOG7F519P.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER3O-419.
YEAST:MONOMER3O-419.
ReactomeiREACT_285133. Sphingolipid de novo biosynthesis.

Miscellaneous databases

NextBioi973636.
PROiP47013.

Gene expression databases

GenevestigatoriP47013.

Family and domain databases

Gene3Di1.20.144.10. 1 hit.
InterProiIPR000326. P_Acid_Pase_2/haloperoxidase.
[Graphical view]
PfamiPF01569. PAP2. 1 hit.
[Graphical view]
SMARTiSM00014. acidPPc. 1 hit.
[Graphical view]
SUPFAMiSSF48317. SSF48317. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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. "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.
  16. "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, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  17. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16 AND SER-18, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  18. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDS1P1_YEAST
AccessioniPrimary (citable) accession number: P47013
Secondary accession number(s): D6VW50
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: April 29, 2015
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

External Data

Dasty 3

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 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.