YDC1_YEAST
ID YDC1_YEAST Reviewed; 317 AA.
AC Q02896; D6W3T0;
DT 14-AUG-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=Alkaline ceramidase YDC1;
DE EC=3.5.1.-;
DE AltName: Full=Acyl-CoA-independent ceramide synthase;
GN Name=YDC1; OrderedLocusNames=YPL087W; ORFNames=LPG21W;
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], FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=10900202; DOI=10.1074/jbc.m003683200;
RA Mao C., Xu R., Bielawska A., Szulc Z.M., Obeid L.M.;
RT "Cloning and characterization of a Saccharomyces cerevisiae alkaline
RT ceramidase with specificity for dihydroceramide.";
RL J. Biol. Chem. 275:31369-31378(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=11694577; DOI=10.1091/mbc.12.11.3417;
RA Schorling S., Vallee B., Barz W.P., Riezman H., Oesterhelt D.;
RT "Lag1p and Lac1p are essential for the acyl-CoA-dependent ceramide synthase
RT reaction in Saccharomyces cerevisae.";
RL Mol. Biol. Cell 12:3417-3427(2001).
RN [6]
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 [7]
RP FUNCTION.
RX PubMed=24866405; DOI=10.1111/1567-1364.12169;
RA Voynova N.S., Mallela S.K., Vazquez H.M., Cerantola V., Sonderegger M.,
RA Knudsen J., Ejsing C.S., Conzelmann A.;
RT "Characterization of yeast mutants lacking alkaline ceramidases YPC1 and
RT YDC1.";
RL FEMS Yeast Res. 14:776-788(2014).
CC -!- FUNCTION: Acyl-CoA-independent ceramide synthase that catalyzes the
CC conversion of dihydroceramide and also phytoceramide to
CC dihydrosphingosine or phytosphingosine. Prefers dihydroceramide. Very
CC low reverse hydrolysis activity, catalyzing synthesis of
CC dihydroceramide from fatty acid and dihydrosphingosine. Is not
CC responsible for the breakdown of unsaturated ceramide. May play a role
CC in heat stress response. {ECO:0000269|PubMed:10900202,
CC ECO:0000269|PubMed:11694577, ECO:0000269|PubMed:24866405}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-hexanoyl-sphinganine = hexanoate + sphinganine;
CC Xref=Rhea:RHEA:38887, ChEBI:CHEBI:15377, ChEBI:CHEBI:17120,
CC ChEBI:CHEBI:57817, ChEBI:CHEBI:76226;
CC Evidence={ECO:0000269|PubMed:10900202};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:38888;
CC Evidence={ECO:0000305|PubMed:10900202};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=hexadecanoate + sphinganine = H2O + N-hexadecanoylsphinganine;
CC Xref=Rhea:RHEA:43440, ChEBI:CHEBI:7896, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:57817, ChEBI:CHEBI:67042;
CC Evidence={ECO:0000269|PubMed:10900202};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:43441;
CC Evidence={ECO:0000305|PubMed:10900202};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-acylsphinganine + H2O = a fatty acid + sphinganine;
CC Xref=Rhea:RHEA:33551, ChEBI:CHEBI:15377, ChEBI:CHEBI:28868,
CC ChEBI:CHEBI:31488, ChEBI:CHEBI:57817;
CC Evidence={ECO:0000269|PubMed:11694577};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:33553;
CC Evidence={ECO:0000305|PubMed:11694577};
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:10900202}; Multi-pass membrane protein
CC {ECO:0000255}.
CC -!- SIMILARITY: Belongs to the alkaline ceramidase family. {ECO:0000305}.
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DR EMBL; AF214455; AAG22594.1; -; Genomic_DNA.
DR EMBL; U43281; AAB68212.1; -; Genomic_DNA.
DR EMBL; AY693224; AAT93243.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11346.1; -; Genomic_DNA.
DR PIR; S61979; S61979.
DR RefSeq; NP_015238.1; NM_001183901.1.
DR AlphaFoldDB; Q02896; -.
DR SMR; Q02896; -.
DR BioGRID; 36094; 70.
DR DIP; DIP-7600N; -.
DR IntAct; Q02896; 10.
DR MINT; Q02896; -.
DR STRING; 4932.YPL087W; -.
DR SwissLipids; SLP:000000929; -.
DR MaxQB; Q02896; -.
DR PaxDb; Q02896; -.
DR PRIDE; Q02896; -.
DR DNASU; 856018; -.
DR EnsemblFungi; YPL087W_mRNA; YPL087W; YPL087W.
DR GeneID; 856018; -.
DR KEGG; sce:YPL087W; -.
DR SGD; S000006008; YDC1.
DR VEuPathDB; FungiDB:YPL087W; -.
DR eggNOG; KOG2329; Eukaryota.
DR GeneTree; ENSGT00730000110920; -.
DR HOGENOM; CLU_063293_3_0_1; -.
DR InParanoid; Q02896; -.
DR OMA; GSMCWLS; -.
DR BioCyc; MetaCyc:YPL087W-MON; -.
DR BioCyc; YEAST:YPL087W-MON; -.
DR BRENDA; 3.5.1.23; 984.
DR Reactome; R-SCE-1660661; Sphingolipid de novo biosynthesis.
DR PRO; PR:Q02896; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q02896; protein.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:SGD.
DR GO; GO:0000329; C:fungal-type vacuole membrane; HDA:SGD.
DR GO; GO:0030176; C:integral component of endoplasmic reticulum membrane; IBA:GO_Central.
DR GO; GO:0071633; F:dihydroceramidase activity; IDA:SGD.
DR GO; GO:0070774; F:phytoceramidase activity; IBA:GO_Central.
DR GO; GO:0046513; P:ceramide biosynthetic process; IGI:SGD.
DR GO; GO:0046514; P:ceramide catabolic process; IMP:SGD.
DR InterPro; IPR008901; ACER.
DR PANTHER; PTHR46187; PTHR46187; 1.
DR Pfam; PF05875; Ceramidase; 1.
PE 1: Evidence at protein level;
KW Disulfide bond; Endoplasmic reticulum; Hydrolase; Membrane;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..317
FT /note="Alkaline ceramidase YDC1"
FT /id="PRO_0000212465"
FT TOPO_DOM 1..35
FT /note="Lumenal"
FT /evidence="ECO:0000305|PubMed:16847258"
FT INTRAMEM 36..56
FT /evidence="ECO:0000250|UniProtKB:P38298"
FT TOPO_DOM 57..67
FT /note="Lumenal"
FT /evidence="ECO:0000305|PubMed:16847258"
FT INTRAMEM 68..88
FT /evidence="ECO:0000250|UniProtKB:P38298"
FT TOPO_DOM 89..98
FT /note="Lumenal"
FT /evidence="ECO:0000305|PubMed:16847258"
FT TRANSMEM 99..121
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 122..133
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305|PubMed:16847258"
FT TRANSMEM 134..156
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 157..160
FT /note="Lumenal"
FT /evidence="ECO:0000305|PubMed:16847258"
FT INTRAMEM 161..181
FT /evidence="ECO:0000250|UniProtKB:P38298"
FT TOPO_DOM 182..195
FT /note="Lumenal"
FT /evidence="ECO:0000305|PubMed:16847258"
FT INTRAMEM 196..216
FT /evidence="ECO:0000250|UniProtKB:P38298"
FT TOPO_DOM 217..239
FT /note="Lumenal"
FT /evidence="ECO:0000305|PubMed:16847258"
FT TRANSMEM 240..262
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 263..317
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:16847258"
FT DISULFID 26..219
FT /evidence="ECO:0000250|UniProtKB:P38298"
SQ SEQUENCE 317 AA; 37231 MW; 57872056DEBE4B69 CRC64;
MLFSWPYPEA PIEGYWGKPT SLIDWCEENY VVSPYIAEWS NTITNSIFLM TAFYSTYSAW
RNKLETRYIL IGMGFSLVGI GSWLFHMTLQ YRYQLLDELP MLYATIIPSW SIFAETQEIL
IKDEKKRKES SFRIQMVISF IMCGIVTILT WIYVVVQKPA IFQVLYGILT LLVVVLSGWL
TYYHVHDSFA KKNLFITMVM GMIPFVIGFI CWQLDIHLCS FWIYIRRTYL ALPLGVLLEL
HAWWHLLTGT GVYIFVVYLQ YLRILTHGNP NDFLFIWRWG FFPELVRKGL PIGTSYSLEY
LGPIVNTQVD DETKKNN
