Serine palmitoyltransferase 1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P25045 (LCB1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 120. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	558 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Lipid metabolism Sphingolipid metabolism
Cellular component	Cytoplasm Endoplasmic reticulum Membrane
Domain	Transmembrane Transmembrane helix
Ligand	Pyridoxal phosphate
Molecular function	Acyltransferase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	sphingolipid biosynthetic process Inferred from mutant phenotype PubMed 1556076. Source: SGD
Cellular_component	SPOTS complex Inferred from direct assay Ref.12. Source: UniProtKB integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro serine C-palmitoyltransferase activity Inferred from mutant phenotype PubMed 1556076. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
LCB2	P40970	9	EBI-10059,EBI-10067

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 558

558

Serine palmitoyltransferase 1

PRO_0000163856

Regions

Topological domain

1 – 49

Lumenal Ref.10

Transmembrane

50 – 84

Helical

Topological domain

85 – 341

257

Cytoplasmic Ref.10

Transmembrane

342 – 371

Helical

Topological domain

372 – 424

Lumenal Ref.10

Transmembrane

425 – 457

Helical

Topological domain

458 – 558

101

Cytoplasmic Ref.10

Amino acid modifications

Modified residue

121

Phosphothreonine Ref.11

Experimental info

Mutagenesis

24 – 26

YLW → DRS: No effect on stability. No effect on LCB2 stabilization.

Mutagenesis

50 – 85

Missing: No effect on stability. No effect on LCB2 stabilization.

Mutagenesis

66 – 68

YGI → DVK: No effect on stability. No effect on LCB2 stabilization.

Mutagenesis

180

C → W or Y: Loss of activity. No effect on interaction with LCB2. Ref.7

Mutagenesis

191

V → D: Loss of activity. No effect on interaction with LCB2. Ref.7

Mutagenesis

342 – 371

Missing: Unstable. Destabilizes LCB2.

Mutagenesis

371 – 386

Missing: No effect on stability. Destabilizes LCB2.

Mutagenesis

386 – 416

Missing: Unstable. Destabilizes LCB2.

Mutagenesis

416 – 425

Missing: No effect on stability. Destabilizes LCB2.

Mutagenesis

433 – 458

Missing: Unstable. Destabilizes LCB2. Ref.10

Mutagenesis

549 – 550

IL → AS: No effect on stability. Partially stabilizes LCB2.

Mutagenesis

549 – 550

IL → PR: No effect on stability. Partially stabilizes LCB2.

Sequence conflict

443

A → P in AAA34739. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

P25045 [UniParc].

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

558

62,207

        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' referencesShow '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. Barrell B.G. Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[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. 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, MASS SPECTROMETRY. 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.
PIR	A43667.
RefSeq	NP_014025.1. NM_001182805.1.
3D structure databases
ProteinModelPortal	P25045.
SMR	P25045. Positions 92-450.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5249N.
IntAct	P25045. 7 interactions.
MINT	MINT-524207.
STRING	4932.YMR296C.
Proteomic databases
PaxDb	P25045.
PeptideAtlas	P25045.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YMR296C; YMR296C; YMR296C.
GeneID	855342.
KEGG	sce:YMR296C.
Organism-specific databases
CYGD	YMR296c.
SGD	S000004911. LCB1.
Phylogenomic databases
eggNOG	COG0156.
GeneTree	ENSGT00550000074872.
HOGENOM	HOG000216602.
KO	K00654.
OMA	EHENLPV.
OrthoDB	EOG4VDT7G.
Enzyme and pathway databases
BioCyc	MetaCyc:YMR296C-MONOMER.
UniPathway	UPA00222.
Gene expression databases
Genevestigator	P25045.
GermOnline	YMR296C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.40.640.10. 1 hit.
InterPro	IPR004839. Aminotransferase_I/II. IPR015424. PyrdxlP-dep_Trfase. IPR015421. PyrdxlP-dep_Trfase_major_sub1. [Graphical view]
Pfam	PF00155. Aminotran_1_2. 1 hit. [Graphical view]
SUPFAM	SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITE	PS00599. AA_TRANSFER_CLASS_2. False negative. [Graphical view]
ProtoNet	Search...
Other
NextBio	979082.

Entry information

Entry name

LCB1_YEAST

Accession

Primary (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:	May 1, 2013
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XIII

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents