Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P40970 (LCB2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 131. 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 2

Short name=SPT 2
EC=2.3.1.50
Alternative name(s):
Long chain base biosynthesis protein 2
Gene names
Name:LCB2
Synonyms:SCS1, TSC1
Ordered Locus Names:YDR062W
ORF Names:D4246, YD9609.16
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length561 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalytic subunit 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.

Catalytic activity

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2. Ref.1 Ref.2 Ref.7 Ref.8 Ref.11

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 LCB1 and TSC3. Ref.2 Ref.7 Ref.8 Ref.11 Ref.12

Subcellular location

Cytoplasm. Endoplasmic reticulum. Membrane; Multi-pass membrane protein Potential Ref.7 Ref.9 Ref.11.

Miscellaneous

Present with 54500 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

LCB1P250459EBI-10067,EBI-10059

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 561561Serine palmitoyltransferase 2
PRO_0000163862

Regions

Transmembrane57 – 7721Helical; Potential
Transmembrane443 – 46321Helical; Potential

Amino acid modifications

Modified residue3661N6-(pyridoxal phosphate)lysine By similarity

Experimental info

Mutagenesis3341H → F: Loss of activity. No effect on interaction with LCB1. Ref.8
Mutagenesis3661K → T: Loss of activity. No effect on interaction with LCB1. Ref.8
Sequence conflict5 – 62AN → PH in AAA53669. Ref.1
Sequence conflict231Q → P in AAA53669. Ref.1
Sequence conflict2361F → S in AAU09688. Ref.6
Sequence conflict4411Q → K in AAA53669. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P40970 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 06DF4A709CC9F29B

FASTA56163,111
        10         20         30         40         50         60 
MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE PVVDTPPYYI 

        70         80         90        100        110        120 
SLLTYLNYLI LIILGHVHDF LGMTFQKNKH LDLLEHDGLA PWFSNFESFY VRRIKMRIDD 

       130        140        150        160        170        180 
CFSRPTTGVP GRFIRCIDRI SHNINEYFTY SGAVYPCMNL SSYNYLGFAQ SKGQCTDAAL 

       190        200        210        220        230        240 
ESVDKYSIQS GGPRAQIGTT DLHIKAEKLV ARFIGKEDAL VFSMGYGTNA NLFNAFLDKK 

       250        260        270        280        290        300 
CLVISDELNH TSIRTGVRLS GAAVRTFKHG DMVGLEKLIR EQIVLGQPKT NRPWKKILIC 

       310        320        330        340        350        360 
AEGLFSMEGT LCNLPKLVEL KKKYKCYLFI DEAHSIGAMG PTGRGVCEIF GVDPKDVDIL 

       370        380        390        400        410        420 
MGTFTKSFGA AGGYIAADQW IIDRLRLDLT TVSYSESMPA PVLAQTISSL QTISGEICPG 

       430        440        450        460        470        480 
QGTERLQRIA FNSRYLRLAL QRLGFIVYGV ADSPVIPLLL YCPSKMPAFS RMMLQRRIAV 

       490        500        510        520        530        540 
VVVAYPATPL IESRVRFCMS ASLTKEDIDY LLRHVSEVGD KLNLKSNSGK SSYDGKRQRW 

       550        560 
DIEEVIRRTP EDCKDDKYFV N 

« Hide

References

« Hide 'large scale' references
[1]"Suppressors of the Ca(2+)-sensitive yeast mutant (csg2) identify genes involved in sphingolipid biosynthesis. Cloning and characterization of SCS1, a gene required for serine palmitoyltransferase activity."
Zhao C., Beeler T., Dunn T.
J. Biol. Chem. 269:21480-21488(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ENZYME ACTIVITY.
[2]"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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ENZYME ACTIVITY, SUBUNIT.
Strain: ATCC 26109 / X2180.
[3]"Nucleotide sequence analysis of a 32,500 bp region of the right arm of Saccharomyces cerevisiae chromosome IV."
Brandt P., Ramlow S., Otto B., Bloecker H.
Yeast 12:85-90(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. expand/collapse author list , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[6]"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.
[7]"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 LCB1 AND TSC3, SUBCELLULAR LOCATION.
[8]"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: ENZYME ACTIVITY, INTERACTION WITH LCB1, SUBUNIT, MUTAGENESIS OF HIS-334 AND LYS-366.
[9]"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].
[10]"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].
[11]"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 LCB1, SUBCELLULAR LOCATION.
[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
L33931 Genomic DNA. Translation: AAA53669.1.
M95669 Genomic DNA. Translation: AAA34740.1.
X84162 Genomic DNA. Translation: CAA58978.1.
Z49209 Genomic DNA. Translation: CAA89091.1.
Z74358 Genomic DNA. Translation: CAA98880.1.
AY723771 Genomic DNA. Translation: AAU09688.1.
BK006938 Genomic DNA. Translation: DAA11908.1.
PIRS54046.
RefSeqNP_010347.1. NM_001180370.1.

3D structure databases

ProteinModelPortalP40970.
SMRP40970. Positions 123-524.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32117. 65 interactions.
DIPDIP-6658N.
IntActP40970. 31 interactions.
MINTMINT-616393.
STRING4932.YDR062W.

Proteomic databases

PaxDbP40970.
PeptideAtlasP40970.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDR062W; YDR062W; YDR062W.
GeneID851634.
KEGGsce:YDR062W.

Organism-specific databases

CYGDYDR062w.
SGDS000002469. LCB2.

Phylogenomic databases

eggNOGCOG0156.
GeneTreeENSGT00550000074678.
HOGENOMHOG000206826.
KOK00654.
OMAPEPGGCC.
OrthoDBEOG7XPZG0.

Enzyme and pathway databases

BioCycMetaCyc:YDR062W-MONOMER.
YEAST:YDR062W-MONOMER.
UniPathwayUPA00222.

Gene expression databases

GenevestigatorP40970.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProIPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 1 hit.
PROSITEPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio969188.
PROP40970.

Entry information

Entry nameLCB2_YEAST
AccessionPrimary (citable) accession number: P40970
Secondary accession number(s): D6VS48, Q66RG8
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: April 16, 2014
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: 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