ID DS1P1_YEAST Reviewed; 409 AA. AC P47013; D6VW50; DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot. DT 01-FEB-1996, sequence version 1. DT 24-JAN-2024, entry version 174. DE RecName: Full=Dihydrosphingosine 1-phosphate phosphatase LCB3 {ECO:0000303|PubMed:9195906}; DE EC=3.1.3.- {ECO:0000269|PubMed:25345524}; DE AltName: Full=Long-chain base protein 3 {ECO:0000303|PubMed:9195906}; DE AltName: Full=Sphingolipid resistance protein 2 {ECO:0000303|PubMed:9353337}; GN Name=LCB3 {ECO:0000303|PubMed:9195906}; GN Synonyms=LBP1 {ECO:0000303|PubMed:9419344}, YSR2 GN {ECO:0000303|PubMed:9353337}; OrderedLocusNames=YJL134W; GN ORFNames=J0671; OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast). OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; OC Saccharomycetales; Saccharomycetaceae; Saccharomyces. OX NCBI_TaxID=559292; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=ATCC 96604 / S288c / FY1679; RX PubMed=8813765; RX DOI=10.1002/(sici)1097-0061(19960630)12:8<787::aid-yea954>3.0.co;2-4; RA Katsoulou C., Tzermia M., Tavernarakis N., Alexandraki D.; RT "Sequence analysis of a 40.7 kb segment from the left arm of yeast RT chromosome X reveals 14 known genes and 13 new open reading frames RT including homologues of genes clustered on the right arm of chromosome RT XI."; RL Yeast 12:787-797(1996). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x; RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.; RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."; RL EMBO J. 15:2031-2049(1996). RN [3] RP GENOME REANNOTATION. RC STRAIN=ATCC 204508 / S288c; RX PubMed=24374639; DOI=10.1534/g3.113.008995; RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.; RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now."; RL G3 (Bethesda) 4:389-398(2014). RN [4] RP FUNCTION. RX PubMed=9195906; DOI=10.1074/jbc.272.26.16110; RA Qie L., Nagiec M.M., Baltisberger J.A., Lester R.L., Dickson R.C.; RT "Identification of a Saccharomyces gene, LCB3, necessary for incorporation RT of exogenous long chain bases into sphingolipids."; RL J. Biol. Chem. 272:16110-16117(1997). RN [5] RP FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION. RX PubMed=9353337; DOI=10.1074/jbc.272.45.28690; RA Mao C., Wadleigh M., Jenkins G.M., Hannun Y.A., Obeid L.M.; RT "Identification and characterization of Saccharomyces cerevisiae RT dihydrosphingosine-1-phosphate phosphatase."; RL J. Biol. Chem. 272:28690-28694(1997). RN [6] RP FUNCTION. RX PubMed=9419344; DOI=10.1073/pnas.95.1.150; RA Mandala S.M., Thornton R., Tu Z., Kurtz M.B., Nickels J., Broach J., RA Menzeleev R., Spiegel S.; RT "Sphingoid base 1-phosphate phosphatase: a key regulator of sphingolipid RT metabolism and stress response."; RL Proc. Natl. Acad. Sci. U.S.A. 95:150-155(1998). RN [7] RP FUNCTION, AND SUBCELLULAR LOCATION. RX PubMed=10477278; DOI=10.1042/bj3420667; RA Mao C., Saba J.D., Obeid L.M.; RT "The dihydrosphingosine-1-phosphate phosphatases of Saccharomyces RT cerevisiae are important regulators of cell proliferation and heat stress RT responses."; RL Biochem. J. 342:667-675(1999). RN [8] RP FUNCTION. RX PubMed=10856228; DOI=10.1093/emboj/19.12.2824; RA Zanolari B., Friant S., Funato K., Suetterlin C., Stevenson B.J., RA Riezman H.; RT "Sphingoid base synthesis requirement for endocytosis in Saccharomyces RT cerevisiae."; RL EMBO J. 19:2824-2833(2000). RN [9] RP FUNCTION, AND SUBCELLULAR LOCATION. RX PubMed=10563329; DOI=10.1016/s0076-6879(00)11085-7; RA Mao C., Obeid L.M.; RT "Yeast sphingosine-1-phosphate phosphatases: assay, expression, deletion, RT purification, and cellular localization by GFP tagging."; RL Methods Enzymol. 311:223-232(2000). RN [10] RP FUNCTION. RX PubMed=11278643; DOI=10.1074/jbc.m010221200; RA Birchwood C.J., Saba J.D., Dickson R.C., Cunningham K.W.; RT "Calcium influx and signaling in yeast stimulated by intracellular RT sphingosine 1-phosphate accumulation."; RL J. Biol. Chem. 276:11712-11718(2001). RN [11] RP FUNCTION. RX PubMed=11967828; DOI=10.1002/yea.861; RA Ferguson-Yankey S.R., Skrzypek M.S., Lester R.L., Dickson R.C.; RT "Mutant analysis reveals complex regulation of sphingolipid long chain base RT phosphates and long chain bases during heat stress in yeast."; RL Yeast 19:573-586(2002). RN [12] RP FUNCTION. RX PubMed=12684378; DOI=10.1128/ec.2.2.284-294.2003; RA Kobayashi S.D., Nagiec M.M.; RT "Ceramide/long-chain base phosphate rheostat in Saccharomyces cerevisiae: RT regulation of ceramide synthesis by Elo3p and Cka2p."; RL Eukaryot. Cell 2:284-294(2003). RN [13] RP FUNCTION, MUTAGENESIS OF LYS-128; HIS-160 AND HIS-210, GLYCOSYLATION, AND RP TOPOLOGY. RX PubMed=12786943; DOI=10.1046/j.1365-2443.2003.00653.x; RA Kihara A., Sano T., Iwaki S., Igarashi Y.; RT "Transmembrane topology of sphingoid long-chain base-1-phosphate RT phosphatase, Lcb3p."; RL Genes Cells 8:525-535(2003). RN [14] RP FUNCTION. RX PubMed=12493772; DOI=10.1074/jbc.m209925200; RA Funato K., Lombardi R., Vallee B., Riezman H.; RT "Lcb4p is a key regulator of ceramide synthesis from exogenous long chain RT sphingoid base in Saccharomyces cerevisiae."; RL J. Biol. Chem. 278:7325-7334(2003). RN [15] RP TOPOLOGY [LARGE SCALE ANALYSIS]. RC STRAIN=ATCC 208353 / W303-1A; RX PubMed=16847258; DOI=10.1073/pnas.0604075103; RA Kim H., Melen K., Oesterberg M., von Heijne G.; RT "A global topology map of the Saccharomyces cerevisiae membrane proteome."; RL Proc. Natl. Acad. Sci. U.S.A. 103:11142-11147(2006). RN [16] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16 AND SER-18, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC STRAIN=ADR376; RX PubMed=17330950; DOI=10.1021/pr060559j; RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., RA Elias J.E., Gygi S.P.; RT "Large-scale phosphorylation analysis of alpha-factor-arrested RT Saccharomyces cerevisiae."; RL J. Proteome Res. 6:1190-1197(2007). RN [17] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16 AND SER-18, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19779198; DOI=10.1126/science.1172867; RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.; RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights RT into evolution."; RL Science 325:1682-1686(2009). RN [18] RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=22814378; DOI=10.1073/pnas.1210303109; RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.; RT "N-terminal acetylome analyses and functional insights of the N-terminal RT acetyltransferase NatB."; RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012). RN [19] RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES. RX PubMed=25345524; DOI=10.1038/ncomms6338; RA Kondo N., Ohno Y., Yamagata M., Obara T., Seki N., Kitamura T., RA Naganuma T., Kihara A.; RT "Identification of the phytosphingosine metabolic pathway leading to odd- RT numbered fatty acids."; RL Nat. Commun. 5:5338-5338(2014). CC -!- FUNCTION: Dihydrosphingosine 1-phosphate phosphatase required for CC efficient ceramide synthesis from exogenous sphingoid bases CC (PubMed:10477278, PubMed:10563329, PubMed:10856228, PubMed:11278643, CC PubMed:11967828, PubMed:12493772, PubMed:12684378, PubMed:12786943, CC PubMed:9195906, PubMed:9353337, PubMed:9419344, PubMed:25345524). CC Involved in endocytosis and calcium-mediated signaling CC (PubMed:10856228, PubMed:11278643). {ECO:0000269|PubMed:10477278, CC ECO:0000269|PubMed:10563329, ECO:0000269|PubMed:10856228, CC ECO:0000269|PubMed:11278643, ECO:0000269|PubMed:11967828, CC ECO:0000269|PubMed:12493772, ECO:0000269|PubMed:12684378, CC ECO:0000269|PubMed:12786943, ECO:0000269|PubMed:25345524, CC ECO:0000269|PubMed:9195906, ECO:0000269|PubMed:9353337, CC ECO:0000269|PubMed:9419344}. CC -!- CATALYTIC ACTIVITY: CC Reaction=(4R)-hydroxysphinganine 1-phosphate + H2O = (4R)- CC hydroxysphinganine + phosphate; Xref=Rhea:RHEA:33067, CC ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:64124, CC ChEBI:CHEBI:64795; Evidence={ECO:0000269|PubMed:25345524}; CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33068; CC Evidence={ECO:0000269|PubMed:25345524}; CC -!- CATALYTIC ACTIVITY: CC Reaction=H2O + sphinganine 1-phosphate = phosphate + sphinganine; CC Xref=Rhea:RHEA:27514, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, CC ChEBI:CHEBI:57817, ChEBI:CHEBI:57939; CC Evidence={ECO:0000269|PubMed:25345524, ECO:0000269|PubMed:9353337}; CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27515; CC Evidence={ECO:0000305|PubMed:25345524, ECO:0000305|PubMed:9353337}; CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC Kinetic parameters: CC KM=8.3 uM for dihydrosphingosin 1-phosphate CC {ECO:0000269|PubMed:25345524}; CC KM=17.4 uM for phytosphingosin 1-phosphate CC {ECO:0000269|PubMed:25345524}; CC Vmax=6 nmol/min/ug enzyme toward dihydrosphingosin 1-phosphate CC {ECO:0000269|PubMed:25345524}; CC Vmax=7.3 nmol/min/ug enzyme toward phytosphingosin 1-phosphate CC {ECO:0000269|PubMed:25345524}; CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane CC {ECO:0000269|PubMed:10477278, ECO:0000269|PubMed:10563329, CC ECO:0000269|PubMed:9353337}; Multi-pass membrane protein CC {ECO:0000269|PubMed:10477278, ECO:0000269|PubMed:10563329, CC ECO:0000269|PubMed:9353337}. CC -!- PTM: Glycosylated. {ECO:0000269|PubMed:12786943}. CC -!- SIMILARITY: Belongs to the type 2 lipid phosphate phosphatase family. CC {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X87371; CAA60821.1; -; Genomic_DNA. DR EMBL; Z49410; CAA89430.1; -; Genomic_DNA. DR EMBL; BK006943; DAA08666.1; -; Genomic_DNA. DR PIR; S55178; S55178. DR RefSeq; NP_012401.1; NM_001181567.1. DR AlphaFoldDB; P47013; -. DR BioGRID; 33622; 125. DR DIP; DIP-5685N; -. DR IntAct; P47013; 4. DR MINT; P47013; -. DR STRING; 4932.YJL134W; -. DR SwissLipids; SLP:000000932; -. DR iPTMnet; P47013; -. DR MaxQB; P47013; -. DR PaxDb; 4932-YJL134W; -. DR PeptideAtlas; P47013; -. DR EnsemblFungi; YJL134W_mRNA; YJL134W; YJL134W. DR GeneID; 853307; -. DR KEGG; sce:YJL134W; -. DR AGR; SGD:S000003670; -. DR SGD; S000003670; LCB3. DR VEuPathDB; FungiDB:YJL134W; -. DR eggNOG; KOG2822; Eukaryota. DR GeneTree; ENSGT00660000096503; -. DR HOGENOM; CLU_019266_1_1_1; -. DR InParanoid; P47013; -. DR OMA; CDYIGNC; -. DR OrthoDB; 2958177at2759; -. DR BioCyc; MetaCyc:MONOMER3O-419; -. DR BioCyc; YEAST:MONOMER3O-419; -. DR Reactome; R-SCE-428157; Sphingolipid metabolism. DR BioGRID-ORCS; 853307; 0 hits in 10 CRISPR screens. DR PRO; PR:P47013; -. DR Proteomes; UP000002311; Chromosome X. DR RNAct; P47013; Protein. DR GO; GO:0005783; C:endoplasmic reticulum; IDA:SGD. DR GO; GO:0005789; C:endoplasmic reticulum membrane; IBA:GO_Central. DR GO; GO:0070780; F:dihydrosphingosine-1-phosphate phosphatase activity; IEA:RHEA. DR GO; GO:0042392; F:sphingosine-1-phosphate phosphatase activity; IDA:SGD. DR GO; GO:0019722; P:calcium-mediated signaling; IMP:SGD. DR GO; GO:0046839; P:phospholipid dephosphorylation; IBA:GO_Central. DR GO; GO:0030148; P:sphingolipid biosynthetic process; TAS:SGD. DR CDD; cd03388; PAP2_SPPase1; 1. DR Gene3D; 1.20.144.10; Phosphatidic acid phosphatase type 2/haloperoxidase; 1. DR InterPro; IPR036938; P_Acid_Pase_2/haloperoxi_sf. DR InterPro; IPR000326; P_Acid_Pase_2/haloperoxidase. DR PANTHER; PTHR14969:SF28; DIHYDROSPHINGOSINE 1-PHOSPHATE PHOSPHATASE LCB3-RELATED; 1. DR PANTHER; PTHR14969; SPHINGOSINE-1-PHOSPHATE PHOSPHOHYDROLASE; 1. DR Pfam; PF01569; PAP2; 1. DR SMART; SM00014; acidPPc; 1. DR SUPFAM; SSF48317; Acid phosphatase/Vanadium-dependent haloperoxidase; 1. PE 1: Evidence at protein level; KW Endoplasmic reticulum; Glycoprotein; Hydrolase; Lipid metabolism; Membrane; KW Phosphoprotein; Reference proteome; Sphingolipid metabolism; Transmembrane; KW Transmembrane helix. FT CHAIN 1..409 FT /note="Dihydrosphingosine 1-phosphate phosphatase LCB3" FT /id="PRO_0000203037" FT TOPO_DOM 1..86 FT /note="Lumenal" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 87..107 FT /note="Helical; Name=1" FT /evidence="ECO:0000255" FT TOPO_DOM 108..112 FT /note="Cytoplasmic" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 113..133 FT /note="Helical; Name=2" FT /evidence="ECO:0000255" FT TOPO_DOM 134..182 FT /note="Lumenal" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 183..203 FT /note="Helical; Name=3" FT /evidence="ECO:0000255" FT TOPO_DOM 204..207 FT /note="Cytoplasmic" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 208..228 FT /note="Helical; Name=4" FT /evidence="ECO:0000255" FT TOPO_DOM 229..245 FT /note="Lumenal" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 246..266 FT /note="Helical; Name=5" FT /evidence="ECO:0000255" FT TOPO_DOM 267..276 FT /note="Cytoplasmic" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 277..297 FT /note="Helical; Name=6" FT /evidence="ECO:0000255" FT TOPO_DOM 298..315 FT /note="Lumenal" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 316..336 FT /note="Helical; Name=7" FT /evidence="ECO:0000255" FT TOPO_DOM 337..384 FT /note="Cytoplasmic" FT /evidence="ECO:0000305|PubMed:16847258" FT TRANSMEM 385..405 FT /note="Helical; Name=8" FT /evidence="ECO:0000255" FT TOPO_DOM 406..409 FT /note="Lumenal" FT /evidence="ECO:0000269|PubMed:16847258" FT REGION 15..35 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 128..136 FT /note="Phosphatase sequence motif I" FT /evidence="ECO:0000305" FT REGION 157..160 FT /note="Phosphatase sequence motif II" FT /evidence="ECO:0000305" FT REGION 203..214 FT /note="Phosphatase sequence motif III" FT /evidence="ECO:0000305" FT ACT_SITE 160 FT /note="Proton donor" FT /evidence="ECO:0000250|UniProtKB:P0A924" FT ACT_SITE 210 FT /note="Nucleophile" FT /evidence="ECO:0000250|UniProtKB:P0A924" FT SITE 214 FT /note="Stabilizes the active site histidine for FT nucleophilic attack" FT /evidence="ECO:0000250|UniProtKB:P0A924" FT MOD_RES 16 FT /note="Phosphothreonine" FT /evidence="ECO:0007744|PubMed:17330950, FT ECO:0007744|PubMed:19779198" FT MOD_RES 18 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:17330950, FT ECO:0007744|PubMed:19779198" FT MUTAGEN 128 FT /note="K->A: Impairs dihydrosphingosine 1-phosphate FT phosphatase activity." FT /evidence="ECO:0000269|PubMed:12786943" FT MUTAGEN 160 FT /note="H->A: Impairs dihydrosphingosine 1-phosphate FT phosphatase activity." FT /evidence="ECO:0000269|PubMed:12786943" FT MUTAGEN 210 FT /note="H->A: Impairs dihydrosphingosine 1-phosphate FT phosphatase activity." FT /evidence="ECO:0000269|PubMed:12786943" SQ 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 //