LCB2_YEAST
ID LCB2_YEAST Reviewed; 561 AA.
AC P40970; D6VS48; Q66RG8;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=Serine palmitoyltransferase 2;
DE Short=SPT 2;
DE EC=2.3.1.50;
DE AltName: Full=Long chain base biosynthesis protein 2;
GN Name=LCB2; Synonyms=SCS1, TSC1; OrderedLocusNames=YDR062W;
GN ORFNames=D4246, YD9609.16;
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], AND ENZYME ACTIVITY.
RX PubMed=8063782; DOI=10.1016/s0021-9258(17)31829-x;
RA Zhao C., Beeler T., Dunn T.;
RT "Suppressors of the Ca(2+)-sensitive yeast mutant (csg2) identify genes
RT involved in sphingolipid biosynthesis. Cloning and characterization of
RT SCS1, a gene required for serine palmitoyltransferase activity.";
RL J. Biol. Chem. 269:21480-21488(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], ENZYME ACTIVITY, AND SUBUNIT.
RC STRAIN=ATCC 26109 / X2180;
RX PubMed=8058731; DOI=10.1073/pnas.91.17.7899;
RA Nagiec M.M., Baltisberger J.A., Wells G.B., Lester R.L., Dickson R.C.;
RT "The LCB2 gene of Saccharomyces and the related LCB1 gene encode subunits
RT of serine palmitoyltransferase, the initial enzyme in sphingolipid
RT synthesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 91:7899-7902(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8789263;
RX DOI=10.1002/(sici)1097-0061(199601)12:1<85::aid-yea890>3.0.co;2-u;
RA Brandt P., Ramlow S., Otto B., Bloecker H.;
RT "Nucleotide sequence analysis of a 32,500 bp region of the right arm of
RT Saccharomyces cerevisiae chromosome IV.";
RL Yeast 12:85-90(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [5]
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 [6]
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 [7]
RP ENZYME ACTIVITY, INTERACTION WITH LCB1 AND TSC3, AND SUBCELLULAR LOCATION.
RX PubMed=10713067; DOI=10.1074/jbc.275.11.7597;
RA Gable K., Slife H., Bacikova D., Monaghan E., Dunn T.M.;
RT "Tsc3p is an 80-amino acid protein associated with serine
RT palmitoyltransferase and required for optimal enzyme activity.";
RL J. Biol. Chem. 275:7597-7603(2000).
RN [8]
RP ENZYME ACTIVITY, INTERACTION WITH LCB1, SUBUNIT, AND MUTAGENESIS OF HIS-334
RP AND LYS-366.
RX PubMed=11781309; DOI=10.1074/jbc.m107873200;
RA Gable K., Han G., Monaghan E., Bacikova D., Natarajan M., Williams R.,
RA Dunn T.M.;
RT "Mutations in the yeast LCB1 and LCB2 genes, including those corresponding
RT to the hereditary sensory neuropathy type I mutations, dominantly
RT inactivate serine palmitoyltransferase.";
RL J. Biol. Chem. 277:10194-10200(2002).
RN [9]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP ENZYME ACTIVITY, INTERACTION WITH LCB1, AND SUBCELLULAR LOCATION.
RX PubMed=15485854; DOI=10.1074/jbc.m410014200;
RA Han G., Gable K., Yan L., Natarajan M., Krishnamurthy J., Gupta S.D.,
RA Borovitskaya A., Harmon J.M., Dunn T.M.;
RT "The topology of the Lcb1p subunit of yeast serine palmitoyltransferase.";
RL J. Biol. Chem. 279:53707-53716(2004).
RN [12]
RP IDENTIFICATION IN THE SPOTS COMPLEX.
RX PubMed=20182505; DOI=10.1038/nature08787;
RA Breslow D.K., Collins S.R., Bodenmiller B., Aebersold R., Simons K.,
RA Shevchenko A., Ejsing C.S., Weissman J.S.;
RT "Orm family proteins mediate sphingolipid homeostasis.";
RL Nature 463:1048-1053(2010).
CC -!- FUNCTION: Catalytic subunit of serine palmitoyltransferase (SPT), which
CC catalyzes the committed step in the synthesis of sphingolipids, the
CC condensation of serine with palmitoyl CoA to form the long chain base
CC 3-ketosphinganine.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine + CO2 +
CC CoA; Xref=Rhea:RHEA:14761, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57379,
CC ChEBI:CHEBI:58299; EC=2.3.1.50;
CC Evidence={ECO:0000269|PubMed:10713067, ECO:0000269|PubMed:11781309,
CC ECO:0000269|PubMed:15485854, ECO:0000269|PubMed:8058731,
CC ECO:0000269|PubMed:8063782};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC -!- SUBUNIT: LCB1 and LCB2 encode essential subunits of the enzyme and form
CC a heterodimer. Component of the SPOTS complex, at least composed of
CC LCB1/2 (LCB1 and/or LCB2), ORM1/2 (ORM1 and/or ORM2), SAC1 and TSC3.
CC Interacts with LCB1 and TSC3. {ECO:0000269|PubMed:10713067,
CC ECO:0000269|PubMed:11781309, ECO:0000269|PubMed:15485854,
CC ECO:0000269|PubMed:20182505, ECO:0000269|PubMed:8058731}.
CC -!- INTERACTION:
CC P40970; P25045: LCB1; NbExp=9; IntAct=EBI-10067, EBI-10059;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum. Membrane
CC {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 54500 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; L33931; AAA53669.1; -; Genomic_DNA.
DR EMBL; M95669; AAA34740.1; -; Genomic_DNA.
DR EMBL; X84162; CAA58978.1; -; Genomic_DNA.
DR EMBL; Z49209; CAA89091.1; -; Genomic_DNA.
DR EMBL; Z74358; CAA98880.1; -; Genomic_DNA.
DR EMBL; AY723771; AAU09688.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11908.1; -; Genomic_DNA.
DR PIR; S54046; S54046.
DR RefSeq; NP_010347.1; NM_001180370.1.
DR AlphaFoldDB; P40970; -.
DR SMR; P40970; -.
DR BioGRID; 32117; 628.
DR ComplexPortal; CPX-3158; SPOTS complex.
DR DIP; DIP-6658N; -.
DR IntAct; P40970; 33.
DR MINT; P40970; -.
DR STRING; 4932.YDR062W; -.
DR MaxQB; P40970; -.
DR PaxDb; P40970; -.
DR PRIDE; P40970; -.
DR EnsemblFungi; YDR062W_mRNA; YDR062W; YDR062W.
DR GeneID; 851634; -.
DR KEGG; sce:YDR062W; -.
DR SGD; S000002469; LCB2.
DR VEuPathDB; FungiDB:YDR062W; -.
DR eggNOG; KOG1357; Eukaryota.
DR GeneTree; ENSGT00940000168104; -.
DR HOGENOM; CLU_015846_7_2_1; -.
DR InParanoid; P40970; -.
DR OMA; IEDEPPY; -.
DR BioCyc; MetaCyc:YDR062W-MON; -.
DR BioCyc; YEAST:YDR062W-MON; -.
DR UniPathway; UPA00222; -.
DR PRO; PR:P40970; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P40970; protein.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:SGD.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0017059; C:serine C-palmitoyltransferase complex; IBA:GO_Central.
DR GO; GO:0035339; C:SPOTS complex; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0004758; F:serine C-palmitoyltransferase activity; IMP:SGD.
DR GO; GO:0090156; P:cellular sphingolipid homeostasis; IC:ComplexPortal.
DR GO; GO:0046513; P:ceramide biosynthetic process; IBA:GO_Central.
DR GO; GO:0030148; P:sphingolipid biosynthetic process; IMP:SGD.
DR GO; GO:0046512; P:sphingosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR001917; Aminotrans_II_pyridoxalP_BS.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1.
PE 1: Evidence at protein level;
KW Acyltransferase; Cytoplasm; Endoplasmic reticulum; Lipid metabolism;
KW Membrane; Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..561
FT /note="Serine palmitoyltransferase 2"
FT /id="PRO_0000163862"
FT TRANSMEM 57..77
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 443..463
FT /note="Helical"
FT /evidence="ECO:0000255"
FT MOD_RES 366
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT MUTAGEN 334
FT /note="H->F: Loss of activity. No effect on interaction
FT with LCB1."
FT /evidence="ECO:0000269|PubMed:11781309"
FT MUTAGEN 366
FT /note="K->T: Loss of activity. No effect on interaction
FT with LCB1."
FT /evidence="ECO:0000269|PubMed:11781309"
FT CONFLICT 5..6
FT /note="AN -> PH (in Ref. 1; AAA53669)"
FT /evidence="ECO:0000305"
FT CONFLICT 23
FT /note="Q -> P (in Ref. 1; AAA53669)"
FT /evidence="ECO:0000305"
FT CONFLICT 236
FT /note="F -> S (in Ref. 6; AAU09688)"
FT /evidence="ECO:0000305"
FT CONFLICT 441
FT /note="Q -> K (in Ref. 1; AAA53669)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 561 AA; 63111 MW; 06DF4A709CC9F29B CRC64;
MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE PVVDTPPYYI
SLLTYLNYLI LIILGHVHDF LGMTFQKNKH LDLLEHDGLA PWFSNFESFY VRRIKMRIDD
CFSRPTTGVP GRFIRCIDRI SHNINEYFTY SGAVYPCMNL SSYNYLGFAQ SKGQCTDAAL
ESVDKYSIQS GGPRAQIGTT DLHIKAEKLV ARFIGKEDAL VFSMGYGTNA NLFNAFLDKK
CLVISDELNH TSIRTGVRLS GAAVRTFKHG DMVGLEKLIR EQIVLGQPKT NRPWKKILIC
AEGLFSMEGT LCNLPKLVEL KKKYKCYLFI DEAHSIGAMG PTGRGVCEIF GVDPKDVDIL
MGTFTKSFGA AGGYIAADQW IIDRLRLDLT TVSYSESMPA PVLAQTISSL QTISGEICPG
QGTERLQRIA FNSRYLRLAL QRLGFIVYGV ADSPVIPLLL YCPSKMPAFS RMMLQRRIAV
VVVAYPATPL IESRVRFCMS ASLTKEDIDY LLRHVSEVGD KLNLKSNSGK SSYDGKRQRW
DIEEVIRRTP EDCKDDKYFV N
