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Protein

Serine palmitoyltransferase 1

Gene

LCB1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

Pathwayi: sphingolipid metabolism

This protein is involved in the pathway sphingolipid metabolism, which is part of Lipid metabolism.
View all proteins of this organism that are known to be involved in the pathway sphingolipid metabolism and in Lipid metabolism.

GO - Molecular functioni

  • pyridoxal phosphate binding Source: InterPro
  • serine C-palmitoyltransferase activity Source: SGD

GO - Biological processi

  • 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.
ReactomeiR-SCE-1660661. 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
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR296C.
SGDiS000004911. LCB1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 4949Lumenal1 PublicationAdd
BLAST
Transmembranei50 – 8435HelicalAdd
BLAST
Topological domaini85 – 341257Cytoplasmic1 PublicationAdd
BLAST
Transmembranei342 – 37130HelicalAdd
BLAST
Topological domaini372 – 42453Lumenal1 PublicationAdd
BLAST
Transmembranei425 – 45733HelicalAdd
BLAST
Topological domaini458 – 558101Cytoplasmic1 PublicationAdd
BLAST

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB-KW
  • serine C-palmitoyltransferase complex Source: SGD
  • 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 – 1211PhosphothreonineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP25045.

PTM databases

iPTMnetiP25045.

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.

Structurei

3D structure databases

ProteinModelPortaliP25045.
SMRiP25045. Positions 92-449.
ModBaseiSearch...
MobiDBiSearch...

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

GeneTreeiENSGT00550000074872.
HOGENOMiHOG000216602.
InParanoidiP25045.
KOiK00654.
OMAiGCIVYAQ.
OrthoDBiEOG092C2DQ1.

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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP25045.
SMRiP25045. Positions 92-449.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP25045.

Proteomic databases

MaxQBiP25045.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YMR296C.
SGDiS000004911. LCB1.

Phylogenomic databases

GeneTreeiENSGT00550000074872.
HOGENOMiHOG000216602.
InParanoidiP25045.
KOiK00654.
OMAiGCIVYAQ.
OrthoDBiEOG092C2DQ1.

Enzyme and pathway databases

UniPathwayiUPA00222.
BioCyciMetaCyc:YMR296C-MONOMER.
YEAST:YMR296C-MONOMER.
ReactomeiR-SCE-1660661. Sphingolipid de novo biosynthesis.

Miscellaneous databases

PROiP25045.

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.
ProtoNetiSearch...

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: September 7, 2016
This is version 150 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.