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P25045

- LCB1_YEAST

UniProt

P25045 - LCB1_YEAST

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Protein

Serine palmitoyltransferase 1

Gene

LCB1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.4 Publications

Cofactori

Pyridoxal phosphate.

Pathwayi

GO - Molecular functioni

  1. pyridoxal phosphate binding Source: InterPro
  2. serine C-palmitoyltransferase activity Source: SGD

GO - Biological processi

  1. sphingolipid biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:YMR296C-MONOMER.
YEAST:YMR296C-MONOMER.
ReactomeiREACT_189220. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine palmitoyltransferase 1 (EC:2.3.1.50)
Short name:
SPT 1
Short name:
SPT1
Alternative name(s):
Long chain base biosynthesis protein 1
Gene namesi
Name:LCB1
Synonyms:END8, TSC2
Ordered Locus Names:YMR296C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIII

Organism-specific databases

CYGDiYMR296c.
SGDiS000004911. LCB1.

Subcellular locationi

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. serine C-palmitoyltransferase complex Source: SGD
  3. SPOTS complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi24 – 263YLW → DRS: No effect on stability. No effect on LCB2 stabilization. 1 Publication
Mutagenesisi50 – 8536Missing: No effect on stability. No effect on LCB2 stabilization. 1 PublicationAdd
BLAST
Mutagenesisi66 – 683YGI → DVK: No effect on stability. No effect on LCB2 stabilization. 1 Publication
Mutagenesisi180 – 1801C → W or Y: Loss of activity. No effect on interaction with LCB2. 1 Publication
Mutagenesisi191 – 1911V → D: Loss of activity. No effect on interaction with LCB2. 1 Publication
Mutagenesisi342 – 37130Missing: Unstable. Destabilizes LCB2. 1 PublicationAdd
BLAST
Mutagenesisi371 – 38616Missing: No effect on stability. Destabilizes LCB2. 1 PublicationAdd
BLAST
Mutagenesisi386 – 41631Missing: Unstable. Destabilizes LCB2. 1 PublicationAdd
BLAST
Mutagenesisi416 – 42510Missing: No effect on stability. Destabilizes LCB2. 1 Publication
Mutagenesisi433 – 45826Missing: Unstable. Destabilizes LCB2. 1 PublicationAdd
BLAST
Mutagenesisi549 – 5502IL → AS: No effect on stability. Partially stabilizes LCB2. 1 Publication
Mutagenesisi549 – 5502IL → PR: No effect on stability. Partially stabilizes LCB2. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 558558Serine palmitoyltransferase 1PRO_0000163856Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei121 – 1211Phosphothreonine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP25045.
PaxDbiP25045.
PeptideAtlasiP25045.

Expressioni

Gene expression databases

GenevestigatoriP25045.

Interactioni

Subunit structurei

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 TSC3.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LCB2P409709EBI-10059,EBI-10067

Protein-protein interaction databases

BioGridi35476. 169 interactions.
DIPiDIP-5249N.
IntActiP25045. 8 interactions.
MINTiMINT-524207.
STRINGi4932.YMR296C.

Structurei

3D structure databases

ProteinModelPortaliP25045.
SMRiP25045. Positions 92-450.
ModBaseiSearch...
MobiDBiSearch...

Topological domain

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 4949Lumenal1 PublicationAdd
BLAST
Topological domaini85 – 341257Cytoplasmic1 PublicationAdd
BLAST
Topological domaini372 – 42453Lumenal1 PublicationAdd
BLAST
Topological domaini458 – 558101Cytoplasmic1 PublicationAdd
BLAST

Transmembrane

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei50 – 8435HelicalAdd
BLAST
Transmembranei342 – 37130HelicalAdd
BLAST
Transmembranei425 – 45733HelicalAdd
BLAST

Family & Domainsi

Domaini

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.

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074872.
HOGENOMiHOG000216602.
InParanoidiP25045.
KOiK00654.
OMAiDLVEEWQ.
OrthoDBiEOG7XPZG0.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 2 hits.

Sequencei

Sequence statusi: Complete.

P25045-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAHIPEVLPK SIPIPAFIVT TSSYLWYYFN LVLTQIPGGQ FIVSYIKKSH
60 70 80 90 100
HDDPYRTTVE IGLILYGIIY YLSKPQQKKS LQAQKPNLSP QEIDALIEDW
110 120 130 140 150
EPEPLVDPSA TDEQSWRVAK TPVTMEMPIQ NHITITRNNL QEKYTNVFNL
160 170 180 190 200
ASNNFLQLSA TEPVKEVVKT TIKNYGVGAC GPAGFYGNQD VHYTLEYDLA
210 220 230 240 250
QFFGTQGSVL YGQDFCAAPS VLPAFTKRGD VIVADDQVSL PVQNALQLSR
260 270 280 290 300
STVYYFNHND MNSLECLLNE LTEQEKLEKL PAIPRKFIVT EGIFHNSGDL
310 320 330 340 350
APLPELTKLK NKYKFRLFVD ETFSIGVLGA TGRGLSEHFN MDRATAIDIT
360 370 380 390 400
VGSMATALGS TGGFVLGDSV MCLHQRIGSN AYCFSACLPA YTVTSVSKVL
410 420 430 440 450
KLMDSNNDAV QTLQKLSKSL HDSFASDDSL RSYVIVTSSP VSAVLHLQLT
460 470 480 490 500
PAYRSRKFGY TCEQLFETMS ALQKKSQTNK FIEPYEEEEK FLQSIVDHAL
510 520 530 540 550
INYNVLITRN TIVLKQETLP IVPSLKICCN AAMSPEELKN ACESVKQSIL

ACCQESNK
Length:558
Mass (Da):62,207
Last modified:February 1, 1996 - v2
Checksum:i9F7F93E4B2C70FDB
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti443 – 4431A → P in AAA34739. (PubMed:2066332)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M63674 Genomic DNA. Translation: AAA34739.1.
X80836 Genomic DNA. Translation: CAA56805.1.
AY693052 Genomic DNA. Translation: AAT93071.1.
BK006946 Genomic DNA. Translation: DAA10197.1.
PIRiA43667.
RefSeqiNP_014025.1. NM_001182805.1.

Genome annotation databases

EnsemblFungiiYMR296C; YMR296C; YMR296C.
GeneIDi855342.
KEGGisce:YMR296C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M63674 Genomic DNA. Translation: AAA34739.1 .
X80836 Genomic DNA. Translation: CAA56805.1 .
AY693052 Genomic DNA. Translation: AAT93071.1 .
BK006946 Genomic DNA. Translation: DAA10197.1 .
PIRi A43667.
RefSeqi NP_014025.1. NM_001182805.1.

3D structure databases

ProteinModelPortali P25045.
SMRi P25045. Positions 92-450.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35476. 169 interactions.
DIPi DIP-5249N.
IntActi P25045. 8 interactions.
MINTi MINT-524207.
STRINGi 4932.YMR296C.

Proteomic databases

MaxQBi P25045.
PaxDbi P25045.
PeptideAtlasi P25045.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YMR296C ; YMR296C ; YMR296C .
GeneIDi 855342.
KEGGi sce:YMR296C.

Organism-specific databases

CYGDi YMR296c.
SGDi S000004911. LCB1.

Phylogenomic databases

eggNOGi COG0156.
GeneTreei ENSGT00550000074872.
HOGENOMi HOG000216602.
InParanoidi P25045.
KOi K00654.
OMAi DLVEEWQ.
OrthoDBi EOG7XPZG0.

Enzyme and pathway databases

UniPathwayi UPA00222 .
BioCyci MetaCyc:YMR296C-MONOMER.
YEAST:YMR296C-MONOMER.
Reactomei REACT_189220. Sphingolipid de novo biosynthesis.

Miscellaneous databases

NextBioi 979082.
PROi P25045.

Gene expression databases

Genevestigatori P25045.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
InterProi IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view ]
Pfami PF00155. Aminotran_1_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. 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. Cited for: IDENTIFICATION IN THE SPOTS COMPLEX.

Entry informationi

Entry nameiLCB1_YEAST
AccessioniPrimary (citable) accession number: P25045
Secondary accession number(s): D6W0C3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: February 1, 1996
Last modified: October 29, 2014
This is version 134 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 22400 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3