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P40970

- LCB2_YEAST

UniProt

P40970 - LCB2_YEAST

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Protein
Serine palmitoyltransferase 2
Gene
LCB2, SCS1, TSC1, YDR062W, D4246, YD9609.16
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.5 Publications

Cofactori

Pyridoxal phosphate.

Pathwayi

GO - Molecular functioni

  1. protein binding Source: IntAct
  2. pyridoxal phosphate binding Source: InterPro
  3. 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:YDR062W-MONOMER.
YEAST:YDR062W-MONOMER.
ReactomeiREACT_189220. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine palmitoyltransferase 2 (EC:2.3.1.50)
Short name:
SPT 2
Alternative name(s):
Long chain base biosynthesis protein 2
Gene namesi
Name:LCB2
Synonyms:SCS1, TSC1
Ordered Locus Names:YDR062W
ORF Names:D4246, YD9609.16
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

CYGDiYDR062w.
SGDiS000002469. LCB2.

Subcellular locationi

Cytoplasm. Endoplasmic reticulum. Membrane; Multi-pass membrane protein Reviewed prediction 3 Publications

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei57 – 7721Helical; Reviewed prediction
Add
BLAST
Transmembranei443 – 46321Helical; Reviewed prediction
Add
BLAST

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi334 – 3341H → F: Loss of activity. No effect on interaction with LCB1. 1 Publication
Mutagenesisi366 – 3661K → T: Loss of activity. No effect on interaction with LCB1. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 561561Serine palmitoyltransferase 2
PRO_0000163862Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei366 – 3661N6-(pyridoxal phosphate)lysine By similarity

Proteomic databases

MaxQBiP40970.
PaxDbiP40970.
PeptideAtlasiP40970.

Expressioni

Gene expression databases

GenevestigatoriP40970.

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 LCB1 and TSC3.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LCB1P250459EBI-10067,EBI-10059

Protein-protein interaction databases

BioGridi32117. 65 interactions.
DIPiDIP-6658N.
IntActiP40970. 31 interactions.
MINTiMINT-616393.
STRINGi4932.YDR062W.

Structurei

3D structure databases

ProteinModelPortaliP40970.
SMRiP40970. Positions 158-522.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
KOiK00654.
OMAiPEPGGCC.
OrthoDBiEOG7XPZG0.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR001917. 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]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40970-1 [UniParc]FASTAAdd to Basket

« Hide

MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE    50
PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNKH LDLLEHDGLA 100
PWFSNFESFY VRRIKMRIDD CFSRPTTGVP GRFIRCIDRI SHNINEYFTY 150
SGAVYPCMNL SSYNYLGFAQ SKGQCTDAAL ESVDKYSIQS GGPRAQIGTT 200
DLHIKAEKLV ARFIGKEDAL VFSMGYGTNA NLFNAFLDKK CLVISDELNH 250
TSIRTGVRLS GAAVRTFKHG DMVGLEKLIR EQIVLGQPKT NRPWKKILIC 300
AEGLFSMEGT LCNLPKLVEL KKKYKCYLFI DEAHSIGAMG PTGRGVCEIF 350
GVDPKDVDIL MGTFTKSFGA AGGYIAADQW IIDRLRLDLT TVSYSESMPA 400
PVLAQTISSL QTISGEICPG QGTERLQRIA FNSRYLRLAL QRLGFIVYGV 450
ADSPVIPLLL YCPSKMPAFS RMMLQRRIAV VVVAYPATPL IESRVRFCMS 500
ASLTKEDIDY LLRHVSEVGD KLNLKSNSGK SSYDGKRQRW DIEEVIRRTP 550
EDCKDDKYFV N 561
Length:561
Mass (Da):63,111
Last modified:February 1, 1995 - v1
Checksum:i06DF4A709CC9F29B
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti5 – 62AN → PH in AAA53669. 1 Publication
Sequence conflicti23 – 231Q → P in AAA53669. 1 Publication
Sequence conflicti236 – 2361F → S in AAU09688. 1 Publication
Sequence conflicti441 – 4411Q → K in AAA53669. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiS54046.
RefSeqiNP_010347.1. NM_001180370.1.

Genome annotation databases

EnsemblFungiiYDR062W; YDR062W; YDR062W.
GeneIDi851634.
KEGGisce:YDR062W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi S54046.
RefSeqi NP_010347.1. NM_001180370.1.

3D structure databases

ProteinModelPortali P40970.
SMRi P40970. Positions 158-522.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32117. 65 interactions.
DIPi DIP-6658N.
IntActi P40970. 31 interactions.
MINTi MINT-616393.
STRINGi 4932.YDR062W.

Proteomic databases

MaxQBi P40970.
PaxDbi P40970.
PeptideAtlasi P40970.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDR062W ; YDR062W ; YDR062W .
GeneIDi 851634.
KEGGi sce:YDR062W.

Organism-specific databases

CYGDi YDR062w.
SGDi S000002469. LCB2.

Phylogenomic databases

eggNOGi COG0156.
GeneTreei ENSGT00550000074678.
HOGENOMi HOG000206826.
KOi K00654.
OMAi PEPGGCC.
OrthoDBi EOG7XPZG0.

Enzyme and pathway databases

UniPathwayi UPA00222 .
BioCyci MetaCyc:YDR062W-MONOMER.
YEAST:YDR062W-MONOMER.
Reactomei REACT_189220. Sphingolipid de novo biosynthesis.

Miscellaneous databases

NextBioi 969188.
PROi P40970.

Gene expression databases

Genevestigatori P40970.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProi IPR001917. 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 ]
Pfami PF00155. Aminotran_1_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
PROSITEi PS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. Cited for: ENZYME ACTIVITY, INTERACTION WITH LCB1, SUBCELLULAR LOCATION.
  12. Cited for: IDENTIFICATION IN THE SPOTS COMPLEX.

Entry informationi

Entry nameiLCB2_YEAST
AccessioniPrimary (citable) accession number: P40970
Secondary accession number(s): D6VS48, Q66RG8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 3, 2014
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 54500 molecules/cell in log phase SD medium.

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

External Data

Dasty 3

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