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P25045 (LCB1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Serine palmitoyltransferase 1

Short name=SPT 1
Short name=SPT1
EC=2.3.1.50
Alternative name(s):
Long chain base biosynthesis protein 1
Gene names
Name:LCB1
Synonyms:END8, TSC2
Ordered Locus Names:YMR296C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length558 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.5 Ref.7

Catalytic activity

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2. Ref.5 Ref.6 Ref.7 Ref.10

Cofactor

Pyridoxal phosphate.

Pathway

Lipid metabolism; sphingolipid metabolism.

Subunit structure

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. Ref.5 Ref.6 Ref.7 Ref.10 Ref.12

Subcellular location

Cytoplasm. Endoplasmic reticulum membrane; Multi-pass membrane protein Ref.6 Ref.8 Ref.10.

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. Ref.10

Miscellaneous

Present with 22400 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

LCB2P409709EBI-10059,EBI-10067

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 558558Serine palmitoyltransferase 1
PRO_0000163856

Regions

Topological domain1 – 4949Lumenal Ref.10
Transmembrane50 – 8435Helical
Topological domain85 – 341257Cytoplasmic Ref.10
Transmembrane342 – 37130Helical
Topological domain372 – 42453Lumenal Ref.10
Transmembrane425 – 45733Helical
Topological domain458 – 558101Cytoplasmic Ref.10

Amino acid modifications

Modified residue1211Phosphothreonine Ref.11

Experimental info

Mutagenesis24 – 263YLW → DRS: No effect on stability. No effect on LCB2 stabilization.
Mutagenesis50 – 8536Missing: No effect on stability. No effect on LCB2 stabilization.
Mutagenesis66 – 683YGI → DVK: No effect on stability. No effect on LCB2 stabilization.
Mutagenesis1801C → W or Y: Loss of activity. No effect on interaction with LCB2. Ref.7
Mutagenesis1911V → D: Loss of activity. No effect on interaction with LCB2. Ref.7
Mutagenesis342 – 37130Missing: Unstable. Destabilizes LCB2.
Mutagenesis371 – 38616Missing: No effect on stability. Destabilizes LCB2.
Mutagenesis386 – 41631Missing: Unstable. Destabilizes LCB2.
Mutagenesis416 – 42510Missing: No effect on stability. Destabilizes LCB2.
Mutagenesis433 – 45826Missing: Unstable. Destabilizes LCB2. Ref.10
Mutagenesis549 – 5502IL → AS: No effect on stability. Partially stabilizes LCB2.
Mutagenesis549 – 5502IL → PR: No effect on stability. Partially stabilizes LCB2.
Sequence conflict4431A → P in AAA34739. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P25045 [UniParc].

Last modified February 1, 1996. Version 2.
Checksum: 9F7F93E4B2C70FDB

FASTA55862,207
        10         20         30         40         50         60 
MAHIPEVLPK SIPIPAFIVT TSSYLWYYFN LVLTQIPGGQ FIVSYIKKSH HDDPYRTTVE 

        70         80         90        100        110        120 
IGLILYGIIY YLSKPQQKKS LQAQKPNLSP QEIDALIEDW EPEPLVDPSA TDEQSWRVAK 

       130        140        150        160        170        180 
TPVTMEMPIQ NHITITRNNL QEKYTNVFNL ASNNFLQLSA TEPVKEVVKT TIKNYGVGAC 

       190        200        210        220        230        240 
GPAGFYGNQD VHYTLEYDLA QFFGTQGSVL YGQDFCAAPS VLPAFTKRGD VIVADDQVSL 

       250        260        270        280        290        300 
PVQNALQLSR STVYYFNHND MNSLECLLNE LTEQEKLEKL PAIPRKFIVT EGIFHNSGDL 

       310        320        330        340        350        360 
APLPELTKLK NKYKFRLFVD ETFSIGVLGA TGRGLSEHFN MDRATAIDIT VGSMATALGS 

       370        380        390        400        410        420 
TGGFVLGDSV MCLHQRIGSN AYCFSACLPA YTVTSVSKVL KLMDSNNDAV QTLQKLSKSL 

       430        440        450        460        470        480 
HDSFASDDSL RSYVIVTSSP VSAVLHLQLT PAYRSRKFGY TCEQLFETMS ALQKKSQTNK 

       490        500        510        520        530        540 
FIEPYEEEEK FLQSIVDHAL INYNVLITRN TIVLKQETLP IVPSLKICCN AAMSPEELKN 

       550 
ACESVKQSIL ACCQESNK 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and characterization of LCB1, a Saccharomyces gene required for biosynthesis of the long-chain base component of sphingolipids."
Buede R., Rinker-Schaffer C., Pinto W.J., Lester R.L., Dickson R.C.
J. Bacteriol. 173:4325-4332(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII."
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. expand/collapse author list , Skelton J., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
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. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"The LCB2 gene of Saccharomyces and the related LCB1 gene encode subunits of serine palmitoyltransferase, the initial enzyme in sphingolipid synthesis."
Nagiec M.M., Baltisberger J.A., Wells G.B., Lester R.L., Dickson R.C.
Proc. Natl. Acad. Sci. U.S.A. 91:7899-7902(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME ACTIVITY, SUBUNIT.
[6]"Tsc3p is an 80-amino acid protein associated with serine palmitoyltransferase and required for optimal enzyme activity."
Gable K., Slife H., Bacikova D., Monaghan E., Dunn T.M.
J. Biol. Chem. 275:7597-7603(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME ACTIVITY, INTERACTION WITH LCB2 AND TSC3, SUBCELLULAR LOCATION.
[7]"Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase."
Gable K., Han G., Monaghan E., Bacikova D., Natarajan M., Williams R., Dunn T.M.
J. Biol. Chem. 277:10194-10200(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME ACTIVITY, SUBUNIT, INTERACTION WITH LCB2, MUTAGENESIS OF CYS-180 AND VAL-191.
[8]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]"The topology of the Lcb1p subunit of yeast serine palmitoyltransferase."
Han G., Gable K., Yan L., Natarajan M., Krishnamurthy J., Gupta S.D., Borovitskaya A., Harmon J.M., Dunn T.M.
J. Biol. Chem. 279:53707-53716(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME ACTIVITY, INTERACTION WITH LCB2, SUBCELLULAR LOCATION, TOPOLOGY, TRANSMEMBRANE DOMAINS, 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.
[11]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-121, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[12]"Orm family proteins mediate sphingolipid homeostasis."
Breslow D.K., Collins S.R., Bodenmiller B., Aebersold R., Simons K., Shevchenko A., Ejsing C.S., Weissman J.S.
Nature 463:1048-1053(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE SPOTS COMPLEX.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M63674 Genomic DNA. Translation: AAA34739.1.
X80836 Genomic DNA. Translation: CAA56805.1.
AY693052 Genomic DNA. Translation: AAT93071.1.
BK006946 Genomic DNA. Translation: DAA10197.1.
PIRA43667.
RefSeqNP_014025.1. NM_001182805.1.

3D structure databases

ProteinModelPortalP25045.
SMRP25045. Positions 92-552.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid35476. 167 interactions.
DIPDIP-5249N.
IntActP25045. 8 interactions.
MINTMINT-524207.
STRING4932.YMR296C.

Proteomic databases

PaxDbP25045.
PeptideAtlasP25045.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYMR296C; YMR296C; YMR296C.
GeneID855342.
KEGGsce:YMR296C.

Organism-specific databases

CYGDYMR296c.
SGDS000004911. LCB1.

Phylogenomic databases

eggNOGCOG0156.
GeneTreeENSGT00550000074872.
HOGENOMHOG000216602.
KOK00654.
OMAYGQDFVT.
OrthoDBEOG7XPZG0.

Enzyme and pathway databases

BioCycMetaCyc:YMR296C-MONOMER.
YEAST:YMR296C-MONOMER.
UniPathwayUPA00222.

Gene expression databases

GenevestigatorP25045.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
InterProIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 2 hits.
ProtoNetSearch...

Other

NextBio979082.
PROP25045.

Entry information

Entry nameLCB1_YEAST
AccessionPrimary (citable) accession number: P25045
Secondary accession number(s): D6W0C3
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: February 1, 1996
Last modified: April 16, 2014
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XIII

Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways