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Serine palmitoyltransferase 1 (SPT 1) (SPT1) (EC 2.3.1.50) (Long chain base biosynthesis protein 1)

 LCB1_YEAST              Reviewed;         558 AA.
P25045; D6W0C3;
01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
01-FEB-1996, sequence version 2.
18-JUL-2018, entry version 165.
RecName: Full=Serine palmitoyltransferase 1;
Short=SPT 1;
Short=SPT1;
EC=2.3.1.50;
AltName: Full=Long chain base biosynthesis protein 1;
Name=LCB1; Synonyms=END8, TSC2; OrderedLocusNames=YMR296C;
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].
PubMed=2066332; DOI=10.1128/jb.173.14.4325-4332.1991;
Buede R., Rinker-Schaffer C., Pinto W.J., Lester R.L., Dickson R.C.;
"Cloning and characterization of LCB1, a Saccharomyces gene required
for biosynthesis of the long-chain base component of sphingolipids.";
J. Bacteriol. 173:4325-4332(1991).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169872;
Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S.,
Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A.,
Rice P., Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome
XIII.";
Nature 387:90-93(1997).
[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]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[5]
FUNCTION, ENZYME ACTIVITY, AND SUBUNIT.
PubMed=8058731; DOI=10.1073/pnas.91.17.7899;
Nagiec M.M., Baltisberger J.A., Wells G.B., Lester R.L., Dickson R.C.;
"The LCB2 gene of Saccharomyces and the related LCB1 gene encode
subunits of serine palmitoyltransferase, the initial enzyme in
sphingolipid synthesis.";
Proc. Natl. Acad. Sci. U.S.A. 91:7899-7902(1994).
[6]
ENZYME ACTIVITY, INTERACTION WITH LCB2 AND TSC3, AND SUBCELLULAR
LOCATION.
PubMed=10713067; DOI=10.1074/jbc.275.11.7597;
Gable K., Slife H., Bacikova D., Monaghan E., Dunn T.M.;
"Tsc3p is an 80-amino acid protein associated with serine
palmitoyltransferase and required for optimal enzyme activity.";
J. Biol. Chem. 275:7597-7603(2000).
[7]
FUNCTION, ENZYME ACTIVITY, SUBUNIT, INTERACTION WITH LCB2, AND
MUTAGENESIS OF CYS-180 AND VAL-191.
PubMed=11781309; DOI=10.1074/jbc.M107873200;
Gable K., Han G., Monaghan E., Bacikova D., Natarajan M., Williams R.,
Dunn T.M.;
"Mutations in the yeast LCB1 and LCB2 genes, including those
corresponding to the hereditary sensory neuropathy type I mutations,
dominantly inactivate serine palmitoyltransferase.";
J. Biol. Chem. 277:10194-10200(2002).
[8]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[9]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[10]
ENZYME ACTIVITY, INTERACTION WITH LCB2, SUBCELLULAR LOCATION,
TOPOLOGY, TRANSMEMBRANE DOMAINS, AND MUTAGENESIS OF 24-TYR--TRP-26;
50-ALA--THR-85; 66-TYR--ILE-68; 342-LEU--ARG-371; 371-ARG--HIS-386;
386-HIS--SER-416; 416-SER--TYR-425; 433-GLN--THR-458 AND
549-ILE-LEU-550.
PubMed=15485854; DOI=10.1074/jbc.M410014200;
Han G., Gable K., Yan L., Natarajan M., Krishnamurthy J., Gupta S.D.,
Borovitskaya A., Harmon J.M., Dunn T.M.;
"The topology of the Lcb1p subunit of yeast serine
palmitoyltransferase.";
J. Biol. Chem. 279:53707-53716(2004).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-121, 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).
[12]
IDENTIFICATION IN THE SPOTS COMPLEX.
PubMed=20182505; DOI=10.1038/nature08787;
Breslow D.K., Collins S.R., Bodenmiller B., Aebersold R., Simons K.,
Shevchenko A., Ejsing C.S., Weissman J.S.;
"Orm family proteins mediate sphingolipid homeostasis.";
Nature 463:1048-1053(2010).
-!- FUNCTION: Component of serine palmitoyltransferase (SPT), which
catalyzes the committed step in the synthesis of sphingolipids,
the condensation of serine with palmitoyl CoA to form the long
chain base 3-ketosphinganine. {ECO:0000269|PubMed:11781309,
ECO:0000269|PubMed:8058731}.
-!- CATALYTIC ACTIVITY: Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-
sphinganine + CO(2). {ECO:0000269|PubMed:10713067,
ECO:0000269|PubMed:11781309, ECO:0000269|PubMed:15485854,
ECO:0000269|PubMed:8058731}.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
-!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
-!- SUBUNIT: LCB1 and LCB2 encode essential subunits of the enzyme and
form a heterodimer. Component of the SPOTS complex, at least
composed of LCB1/2 (LCB1 and/or LCB2), ORM1/2 (ORM1 and/or ORM2),
SAC1 and TSC3. Interacts with LCB2 and TSC3.
{ECO:0000269|PubMed:10713067, ECO:0000269|PubMed:11781309,
ECO:0000269|PubMed:15485854, ECO:0000269|PubMed:20182505,
ECO:0000269|PubMed:8058731}.
-!- INTERACTION:
P40970:LCB2; NbExp=9; IntAct=EBI-10059, EBI-10067;
P53224:ORM1; NbExp=5; IntAct=EBI-10059, EBI-12592;
Q06144:ORM2; NbExp=7; IntAct=EBI-10059, EBI-34916;
-!- SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum membrane;
Multi-pass membrane protein.
-!- DOMAIN: The first transmembrane domain is not required for
stability, membrane association, interaction with LCB2, or
enzymatic activity. The second and third transmembrane domains are
required for stability and interaction with LCB2.
-!- MISCELLANEOUS: Present with 22400 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
aminotransferase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; M63674; AAA34739.1; -; Genomic_DNA.
EMBL; X80836; CAA56805.1; -; Genomic_DNA.
EMBL; AY693052; AAT93071.1; -; Genomic_DNA.
EMBL; BK006946; DAA10197.1; -; Genomic_DNA.
PIR; A43667; A43667.
RefSeq; NP_014025.1; NM_001182805.1.
ProteinModelPortal; P25045; -.
BioGrid; 35476; 638.
ComplexPortal; CPX-3158; SPOTS complex.
DIP; DIP-5249N; -.
IntAct; P25045; 16.
MINT; P25045; -.
STRING; 4932.YMR296C; -.
iPTMnet; P25045; -.
MaxQB; P25045; -.
PaxDb; P25045; -.
PRIDE; P25045; -.
EnsemblFungi; YMR296C; YMR296C; YMR296C.
GeneID; 855342; -.
KEGG; sce:YMR296C; -.
EuPathDB; FungiDB:YMR296C; -.
SGD; S000004911; LCB1.
GeneTree; ENSGT00550000074872; -.
HOGENOM; HOG000216602; -.
InParanoid; P25045; -.
KO; K00654; -.
OMA; CVGSHFI; -.
OrthoDB; EOG092C2DQ1; -.
BioCyc; MetaCyc:YMR296C-MONOMER; -.
BioCyc; YEAST:YMR296C-MONOMER; -.
UniPathway; UPA00222; -.
PRO; PR:P25045; -.
Proteomes; UP000002311; Chromosome XIII.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0017059; C:serine C-palmitoyltransferase complex; IMP:SGD.
GO; GO:0035339; C:SPOTS complex; IDA:UniProtKB.
GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
GO; GO:0004758; F:serine C-palmitoyltransferase activity; IMP:SGD.
GO; GO:0030148; P:sphingolipid biosynthetic process; IMP:SGD.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 2.
InterPro; IPR004839; Aminotransferase_I/II.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
Pfam; PF00155; Aminotran_1_2; 1.
SUPFAM; SSF53383; SSF53383; 2.
1: Evidence at protein level;
Acyltransferase; Complete proteome; Cytoplasm; Endoplasmic reticulum;
Lipid metabolism; Membrane; Phosphoprotein; Pyridoxal phosphate;
Reference proteome; Sphingolipid metabolism; Transferase;
Transmembrane; Transmembrane helix.
CHAIN 1 558 Serine palmitoyltransferase 1.
/FTId=PRO_0000163856.
TOPO_DOM 1 49 Lumenal. {ECO:0000269|PubMed:15485854}.
TRANSMEM 50 84 Helical.
TOPO_DOM 85 341 Cytoplasmic.
{ECO:0000269|PubMed:15485854}.
TRANSMEM 342 371 Helical.
TOPO_DOM 372 424 Lumenal. {ECO:0000269|PubMed:15485854}.
TRANSMEM 425 457 Helical.
TOPO_DOM 458 558 Cytoplasmic.
{ECO:0000269|PubMed:15485854}.
MOD_RES 121 121 Phosphothreonine.
{ECO:0000244|PubMed:17330950}.
MUTAGEN 24 26 YLW->DRS: No effect on stability. No
effect on LCB2 stabilization.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 50 85 Missing: No effect on stability. No
effect on LCB2 stabilization.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 66 68 YGI->DVK: No effect on stability. No
effect on LCB2 stabilization.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 180 180 C->W,Y: Loss of activity. No effect on
interaction with LCB2.
{ECO:0000269|PubMed:11781309}.
MUTAGEN 191 191 V->D: Loss of activity. No effect on
interaction with LCB2.
{ECO:0000269|PubMed:11781309}.
MUTAGEN 342 371 Missing: Unstable. Destabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 371 386 Missing: No effect on stability.
Destabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 386 416 Missing: Unstable. Destabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 416 425 Missing: No effect on stability.
Destabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 433 458 Missing: Unstable. Destabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 549 550 IL->AS: No effect on stability. Partially
stabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
MUTAGEN 549 550 IL->PR: No effect on stability. Partially
stabilizes LCB2.
{ECO:0000269|PubMed:15485854}.
CONFLICT 443 443 A -> P (in Ref. 1; AAA34739).
{ECO:0000305}.
SEQUENCE 558 AA; 62207 MW; 9F7F93E4B2C70FDB CRC64;
MAHIPEVLPK SIPIPAFIVT TSSYLWYYFN LVLTQIPGGQ FIVSYIKKSH HDDPYRTTVE
IGLILYGIIY YLSKPQQKKS LQAQKPNLSP QEIDALIEDW EPEPLVDPSA TDEQSWRVAK
TPVTMEMPIQ NHITITRNNL QEKYTNVFNL ASNNFLQLSA TEPVKEVVKT TIKNYGVGAC
GPAGFYGNQD VHYTLEYDLA QFFGTQGSVL YGQDFCAAPS VLPAFTKRGD VIVADDQVSL
PVQNALQLSR STVYYFNHND MNSLECLLNE LTEQEKLEKL PAIPRKFIVT EGIFHNSGDL
APLPELTKLK NKYKFRLFVD ETFSIGVLGA TGRGLSEHFN MDRATAIDIT VGSMATALGS
TGGFVLGDSV MCLHQRIGSN AYCFSACLPA YTVTSVSKVL KLMDSNNDAV QTLQKLSKSL
HDSFASDDSL RSYVIVTSSP VSAVLHLQLT PAYRSRKFGY TCEQLFETMS ALQKKSQTNK
FIEPYEEEEK FLQSIVDHAL INYNVLITRN TIVLKQETLP IVPSLKICCN AAMSPEELKN
ACESVKQSIL ACCQESNK


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