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Dihydrosphingosine 1-phosphate phosphatase LCB3 (EC 3.1.3.-) (Long-chain base protein 3) (Sphingolipid resistance protein 2)

 DS1P1_YEAST             Reviewed;         409 AA.
P47013; D6VW50;
01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
01-FEB-1996, sequence version 1.
31-JAN-2018, entry version 139.
RecName: Full=Dihydrosphingosine 1-phosphate phosphatase LCB3;
EC=3.1.3.-;
AltName: Full=Long-chain base protein 3;
AltName: Full=Sphingolipid resistance protein 2;
Name=LCB3; Synonyms=LBP1, YSR2; OrderedLocusNames=YJL134W;
ORFNames=J0671;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=8813765;
DOI=10.1002/(SICI)1097-0061(19960630)12:8<787::AID-YEA954>3.3.CO;2-W;
Katsoulou C., Tzermia M., Tavernarakis N., Alexandraki D.;
"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.";
Yeast 12:787-797(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8641269;
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.;
"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
X.";
EMBO J. 15:2031-2049(1996).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
FUNCTION.
PubMed=9195906; DOI=10.1074/jbc.272.26.16110;
Qie L., Nagiec M.M., Baltisberger J.A., Lester R.L., Dickson R.C.;
"Identification of a Saccharomyces gene, LCB3, necessary for
incorporation of exogenous long chain bases into sphingolipids.";
J. Biol. Chem. 272:16110-16117(1997).
[5]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=9353337; DOI=10.1074/jbc.272.45.28690;
Mao C., Wadleigh M., Jenkins G.M., Hannun Y.A., Obeid L.M.;
"Identification and characterization of Saccharomyces cerevisiae
dihydrosphingosine-1-phosphate phosphatase.";
J. Biol. Chem. 272:28690-28694(1997).
[6]
FUNCTION.
PubMed=9419344; DOI=10.1073/pnas.95.1.150;
Mandala S.M., Thornton R., Tu Z., Kurtz M.B., Nickels J., Broach J.,
Menzeleev R., Spiegel S.;
"Sphingoid base 1-phosphate phosphatase: a key regulator of
sphingolipid metabolism and stress response.";
Proc. Natl. Acad. Sci. U.S.A. 95:150-155(1998).
[7]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=10477278; DOI=10.1042/bj3420667;
Mao C., Saba J.D., Obeid L.M.;
"The dihydrosphingosine-1-phosphate phosphatases of Saccharomyces
cerevisiae are important regulators of cell proliferation and heat
stress responses.";
Biochem. J. 342:667-675(1999).
[8]
FUNCTION.
PubMed=10856228; DOI=10.1093/emboj/19.12.2824;
Zanolari B., Friant S., Funato K., Suetterlin C., Stevenson B.J.,
Riezman H.;
"Sphingoid base synthesis requirement for endocytosis in Saccharomyces
cerevisiae.";
EMBO J. 19:2824-2833(2000).
[9]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=10563329; DOI=10.1016/S0076-6879(00)11085-7;
Mao C., Obeid L.M.;
"Yeast sphingosine-1-phosphate phosphatases: assay, expression,
deletion, purification, and cellular localization by GFP tagging.";
Methods Enzymol. 311:223-232(2000).
[10]
FUNCTION.
PubMed=11278643; DOI=10.1074/jbc.M010221200;
Birchwood C.J., Saba J.D., Dickson R.C., Cunningham K.W.;
"Calcium influx and signaling in yeast stimulated by intracellular
sphingosine 1-phosphate accumulation.";
J. Biol. Chem. 276:11712-11718(2001).
[11]
FUNCTION.
PubMed=11967828; DOI=10.1002/yea.861;
Ferguson-Yankey S.R., Skrzypek M.S., Lester R.L., Dickson R.C.;
"Mutant analysis reveals complex regulation of sphingolipid long chain
base phosphates and long chain bases during heat stress in yeast.";
Yeast 19:573-586(2002).
[12]
FUNCTION.
PubMed=12684378; DOI=10.1128/EC.2.2.284-294.2003;
Kobayashi S.D., Nagiec M.M.;
"Ceramide/long-chain base phosphate rheostat in Saccharomyces
cerevisiae: regulation of ceramide synthesis by Elo3p and Cka2p.";
Eukaryot. Cell 2:284-294(2003).
[13]
FUNCTION, MUTAGENESIS OF LYS-128; HIS-160 AND HIS-210, GLYCOSYLATION,
AND TOPOLOGY.
PubMed=12786943; DOI=10.1046/j.1365-2443.2003.00653.x;
Kihara A., Sano T., Iwaki S., Igarashi Y.;
"Transmembrane topology of sphingoid long-chain base-1-phosphate
phosphatase, Lcb3p.";
Genes Cells 8:525-535(2003).
[14]
FUNCTION.
PubMed=12493772; DOI=10.1074/jbc.M209925200;
Funato K., Lombardi R., Vallee B., Riezman H.;
"Lcb4p is a key regulator of ceramide synthesis from exogenous long
chain sphingoid base in Saccharomyces cerevisiae.";
J. Biol. Chem. 278:7325-7334(2003).
[15]
TOPOLOGY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 208353 / W303-1A;
PubMed=16847258; DOI=10.1073/pnas.0604075103;
Kim H., Melen K., Oesterberg M., von Heijne G.;
"A global topology map of the Saccharomyces cerevisiae membrane
proteome.";
Proc. Natl. Acad. Sci. U.S.A. 103:11142-11147(2006).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16 AND SER-18, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[17]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16 AND SER-18, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[18]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
-!- FUNCTION: Dihydrosphingosine 1-phosphate phosphatase required for
efficient ceramide synthesis from exogenous sphingoid bases.
Involved in endocytosis and calcium-mediated signaling.
{ECO:0000269|PubMed:10477278, ECO:0000269|PubMed:10563329,
ECO:0000269|PubMed:10856228, ECO:0000269|PubMed:11278643,
ECO:0000269|PubMed:11967828, ECO:0000269|PubMed:12493772,
ECO:0000269|PubMed:12684378, ECO:0000269|PubMed:12786943,
ECO:0000269|PubMed:9195906, ECO:0000269|PubMed:9353337,
ECO:0000269|PubMed:9419344}.
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000269|PubMed:10477278, ECO:0000269|PubMed:10563329,
ECO:0000269|PubMed:9353337}; Multi-pass membrane protein
{ECO:0000269|PubMed:10477278, ECO:0000269|PubMed:10563329,
ECO:0000269|PubMed:9353337}.
-!- PTM: Glycosylated. {ECO:0000269|PubMed:12786943}.
-!- SIMILARITY: Belongs to the type 2 lipid phosphate phosphatase
family. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; X87371; CAA60821.1; -; Genomic_DNA.
EMBL; Z49410; CAA89430.1; -; Genomic_DNA.
EMBL; BK006943; DAA08666.1; -; Genomic_DNA.
PIR; S55178; S55178.
RefSeq; NP_012401.1; NM_001181567.1.
ProteinModelPortal; P47013; -.
BioGrid; 33622; 117.
DIP; DIP-5685N; -.
IntAct; P47013; 4.
MINT; MINT-572017; -.
STRING; 4932.YJL134W; -.
SwissLipids; SLP:000000932; -.
iPTMnet; P47013; -.
MaxQB; P47013; -.
PaxDb; P47013; -.
PRIDE; P47013; -.
EnsemblFungi; YJL134W; YJL134W; YJL134W.
GeneID; 853307; -.
KEGG; sce:YJL134W; -.
EuPathDB; FungiDB:YJL134W; -.
SGD; S000003670; LCB3.
GeneTree; ENSGT00390000017322; -.
HOGENOM; HOG000066080; -.
InParanoid; P47013; -.
KO; K04716; -.
OMA; YKFVTYS; -.
OrthoDB; EOG092C3MDD; -.
BioCyc; MetaCyc:MONOMER3O-419; -.
BioCyc; YEAST:MONOMER3O-419; -.
Reactome; R-SCE-1660661; Sphingolipid de novo biosynthesis.
PRO; PR:P47013; -.
Proteomes; UP000002311; Chromosome X.
GO; GO:0005783; C:endoplasmic reticulum; IDA:SGD.
GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0042392; F:sphingosine-1-phosphate phosphatase activity; IDA:SGD.
GO; GO:0019722; P:calcium-mediated signaling; IMP:SGD.
GO; GO:0030148; P:sphingolipid biosynthetic process; TAS:SGD.
InterPro; IPR036938; P_Acid_Pase_2/haloperoxi_sf.
InterPro; IPR000326; P_Acid_Pase_2/haloperoxidase.
Pfam; PF01569; PAP2; 1.
SMART; SM00014; acidPPc; 1.
SUPFAM; SSF48317; SSF48317; 1.
1: Evidence at protein level;
Complete proteome; Endoplasmic reticulum; Glycoprotein; Hydrolase;
Lipid metabolism; Membrane; Phosphoprotein; Reference proteome;
Sphingolipid metabolism; Transmembrane; Transmembrane helix.
CHAIN 1 409 Dihydrosphingosine 1-phosphate
phosphatase LCB3.
/FTId=PRO_0000203037.
TOPO_DOM 1 86 Lumenal. {ECO:0000305|PubMed:16847258}.
TRANSMEM 87 107 Helical; Name=1. {ECO:0000255}.
TOPO_DOM 108 112 Cytoplasmic.
{ECO:0000305|PubMed:16847258}.
TRANSMEM 113 133 Helical; Name=2. {ECO:0000255}.
TOPO_DOM 134 182 Lumenal. {ECO:0000305|PubMed:16847258}.
TRANSMEM 183 203 Helical; Name=3. {ECO:0000255}.
TOPO_DOM 204 207 Cytoplasmic.
{ECO:0000305|PubMed:16847258}.
TRANSMEM 208 228 Helical; Name=4. {ECO:0000255}.
TOPO_DOM 229 245 Lumenal. {ECO:0000305|PubMed:16847258}.
TRANSMEM 246 266 Helical; Name=5. {ECO:0000255}.
TOPO_DOM 267 276 Cytoplasmic.
{ECO:0000305|PubMed:16847258}.
TRANSMEM 277 297 Helical; Name=6. {ECO:0000255}.
TOPO_DOM 298 315 Lumenal. {ECO:0000305|PubMed:16847258}.
TRANSMEM 316 336 Helical; Name=7. {ECO:0000255}.
TOPO_DOM 337 384 Cytoplasmic.
{ECO:0000305|PubMed:16847258}.
TRANSMEM 385 405 Helical; Name=8. {ECO:0000255}.
TOPO_DOM 406 409 Lumenal. {ECO:0000269|PubMed:16847258}.
REGION 128 136 Phosphatase sequence motif I.
{ECO:0000305}.
REGION 157 160 Phosphatase sequence motif II.
{ECO:0000305}.
REGION 203 214 Phosphatase sequence motif III.
{ECO:0000305}.
ACT_SITE 160 160 Proton donor.
{ECO:0000250|UniProtKB:P0A924}.
ACT_SITE 210 210 Nucleophile.
{ECO:0000250|UniProtKB:P0A924}.
SITE 214 214 Stabilizes the active site histidine for
nucleophilic attack.
{ECO:0000250|UniProtKB:P0A924}.
MOD_RES 16 16 Phosphothreonine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198}.
MOD_RES 18 18 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198}.
MUTAGEN 128 128 K->A: Impairs dihydrosphingosine 1-
phosphate phosphatase activity.
{ECO:0000269|PubMed:12786943}.
MUTAGEN 160 160 H->A: Impairs dihydrosphingosine 1-
phosphate phosphatase activity.
{ECO:0000269|PubMed:12786943}.
MUTAGEN 210 210 H->A: Impairs dihydrosphingosine 1-
phosphate phosphatase activity.
{ECO:0000269|PubMed:12786943}.
SEQUENCE 409 AA; 47372 MW; E0CD7D0F169447C3 CRC64;
MVDGLNTSNI RKRARTLSNP NDFQEPNYLL DPGNHPSDHF RTRMSKFRFN IREKLLVFTN
NQSFTLSRWQ KKYRSAFNDL YFTYTSLMGS HTFYVLCLPM PVWFGYFETT KDMVYILGYS
IYLSGFFKDY WCLPRPRAPP LHRITLSEYT TKEYGAPSSH TANATGVSLL FLYNIWRMQE
SSVMVQLLLS CVVLFYYMTL VFGRIYCGMH GILDLVSGGL IGIVCFIVRM YFKYRFPGLR
IEEHWWFPLF SVGWGLLLLF KHVKPVDECP CFQDSVAFMG VVSGIECCDW LGKVFGVTLV
YNLEPNCGWR LTLARLLVGL PCVVIWKYVI SKPMIYTLLI KVFHLKDDRN VAARKRLEAT
HKEGASKYEC PLYIGEPKID ILGRFIIYAG VPFTVVMCSP VLFSLLNIA


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