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Protein

Serine palmitoyltransferase 2

Gene

LCB2

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

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

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:YDR062W-MONOMER.
YEAST:YDR062W-MONOMER.
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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR062W.
SGDiS000002469. LCB2.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei57 – 77HelicalSequence analysisAdd BLAST21
Transmembranei443 – 463HelicalSequence analysisAdd BLAST21

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)DescriptionActionsGraphical viewLength
Mutagenesisi334H → F: Loss of activity. No effect on interaction with LCB1. 1 Publication1
Mutagenesisi366K → T: Loss of activity. No effect on interaction with LCB1. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001638621 – 561Serine palmitoyltransferase 2Add BLAST561

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei366N6-(pyridoxal phosphate)lysineBy similarity1

Proteomic databases

MaxQBiP40970.
PRIDEiP40970.

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. 67 interactors.
DIPiDIP-6658N.
IntActiP40970. 31 interactors.
MINTiMINT-616393.

Structurei

3D structure databases

ProteinModelPortaliP40970.
SMRiP40970.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
InParanoidiP40970.
KOiK00654.
OMAiKPAAMVF.
OrthoDBiEOG092C2DQ1.

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

        10         20         30         40         50
MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE
60 70 80 90 100
PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNKH LDLLEHDGLA
110 120 130 140 150
PWFSNFESFY VRRIKMRIDD CFSRPTTGVP GRFIRCIDRI SHNINEYFTY
160 170 180 190 200
SGAVYPCMNL SSYNYLGFAQ SKGQCTDAAL ESVDKYSIQS GGPRAQIGTT
210 220 230 240 250
DLHIKAEKLV ARFIGKEDAL VFSMGYGTNA NLFNAFLDKK CLVISDELNH
260 270 280 290 300
TSIRTGVRLS GAAVRTFKHG DMVGLEKLIR EQIVLGQPKT NRPWKKILIC
310 320 330 340 350
AEGLFSMEGT LCNLPKLVEL KKKYKCYLFI DEAHSIGAMG PTGRGVCEIF
360 370 380 390 400
GVDPKDVDIL MGTFTKSFGA AGGYIAADQW IIDRLRLDLT TVSYSESMPA
410 420 430 440 450
PVLAQTISSL QTISGEICPG QGTERLQRIA FNSRYLRLAL QRLGFIVYGV
460 470 480 490 500
ADSPVIPLLL YCPSKMPAFS RMMLQRRIAV VVVAYPATPL IESRVRFCMS
510 520 530 540 550
ASLTKEDIDY LLRHVSEVGD KLNLKSNSGK SSYDGKRQRW DIEEVIRRTP
560
EDCKDDKYFV N
Length:561
Mass (Da):63,111
Last modified:February 1, 1995 - v1
Checksum:i06DF4A709CC9F29B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti5 – 6AN → PH in AAA53669 (PubMed:8063782).Curated2
Sequence conflicti23Q → P in AAA53669 (PubMed:8063782).Curated1
Sequence conflicti236F → S in AAU09688 (PubMed:17322287).Curated1
Sequence conflicti441Q → K in AAA53669 (PubMed:8063782).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP40970.
SMRiP40970.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32117. 67 interactors.
DIPiDIP-6658N.
IntActiP40970. 31 interactors.
MINTiMINT-616393.

Proteomic databases

MaxQBiP40970.
PRIDEiP40970.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YDR062W.
SGDiS000002469. LCB2.

Phylogenomic databases

GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
InParanoidiP40970.
KOiK00654.
OMAiKPAAMVF.
OrthoDBiEOG092C2DQ1.

Enzyme and pathway databases

UniPathwayiUPA00222.
BioCyciMetaCyc:YDR062W-MONOMER.
YEAST:YDR062W-MONOMER.

Miscellaneous databases

PROiP40970.

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]
ProtoNetiSearch...

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: November 2, 2016
This is version 153 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.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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: 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.