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Protein

Serine palmitoyltransferase 3

Gene

sptl-3

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Component of the serine palmitoyltransferase (SPT) that catalyzes the first committed step in sphingolipid biosynthesis, which is the condensation of an acyl-CoA species and L-serine. The catalytic core is composed of a heterodimer of sptl-1 and sptl-2 or sptl-1 and sptl-3 (By similarity). Required for the specification of abicobasal polarity and development of the gut lumen.By similarity1 Publication

Catalytic activityi

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

Cofactori

Pathwayi

GO - Molecular functioni

  1. pyridoxal phosphate binding Source: InterPro
  2. serine C-palmitoyltransferase activity Source: UniProtKB-EC

GO - Biological processi

  1. biosynthetic process Source: InterPro
  2. sphingolipid metabolic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

ReactomeiREACT_183003. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine palmitoyltransferase 3 (EC:2.3.1.50)
Alternative name(s):
Long chain base biosynthesis protein 3
Short name:
LCB 3
Serine-palmitoyl-CoA transferase 3
Short name:
SPT 3
Short name:
SPT3
Gene namesi
Name:sptl-3
ORF Names:T22G5.5
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940: Chromosome V

Organism-specific databases

WormBaseiT22G5.5a; CE31996; WBGene00011932; sptl-3.
T22G5.5b; CE47328; WBGene00011932; sptl-3.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 512512Serine palmitoyltransferase 3PRO_0000421273Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei345 – 3451N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PaxDbiQ9XVI6.

Interactioni

Subunit structurei

Heterodimer of sptl-1/sptl-3.By similarity

Protein-protein interaction databases

DIPiDIP-26788N.
IntActiQ9XVI6. 1 interaction.
MINTiMINT-1127619.
STRINGi6239.T22G5.5.1.

Structurei

3D structure databases

ProteinModelPortaliQ9XVI6.
SMRiQ9XVI6. Positions 133-502.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
InParanoidiQ9XVI6.
OMAiIRRYSAG.
PhylomeDBiQ9XVI6.

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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform a (identifier: Q9XVI6-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGGTQNGKAV ANGKAKNGNI TEKVIKLDPC PKPAFYVFWL VQLNITMMLV
60 70 80 90 100
GAMVATLFDK WGIVKTKRSK GDPRMESFQP LGNSFDATYT DHIYRQSTDV
110 120 130 140 150
VNRPISGVPG AIVRLKDRYT DDHGWTQKYT GTESEVINLG SYNYLGFSHR
160 170 180 190 200
SGVCAEAAAA HIDKYGINCG GSRQEIGNHV AHKSVESTIA QYLNVEDAIV
210 220 230 240 250
FPMGFATNSM NIPSLVDKGS LILSDRLNHA SLVTGCRLSG AHTVVFRHND
260 270 280 290 300
ASDCERKLRD ALCGVSPKTG EKYNKVLIII EGIYSMEGTI VNLPAFIAVK
310 320 330 340 350
KKYNCYLFLD EAHSIGAVGP SGRGVAEYWG CNPRDIDIMM GTLTKSFASA
360 370 380 390 400
GGYMGGSKKV IDHIRRYSAG TCYGVTMSPP LIAQVERAVL IMSGKDGTDI
410 420 430 440 450
GRQKAIQLLE NSRYFRKELR KRGFLVYGNN DSPVVPLMTF YITKVVEFSR
460 470 480 490 500
RMLKHNIGIV AVGYPATPLL EARVRFCLSA DHTKEHLDYI LEAVEQVGME
510
TGTFYGTKIV DE
Length:512
Mass (Da):56,334
Last modified:March 1, 2003 - v2
Checksum:i3F68835D2961C4D0
GO
Isoform b (identifier: Q9XVI6-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MSSCFVFYNM

Show »
Length:521
Mass (Da):57,413
Checksum:i0D69BF15189AF627
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MSSCFVFYNM in isoform b. CuratedVSP_045380

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81127 Genomic DNA. Translation: CAB03390.2.
Z81127 Genomic DNA. Translation: CCG28222.1.
PIRiT25126.
RefSeqiNP_001256547.1. NM_001269618.1. [Q9XVI6-2]
NP_001256548.1. NM_001269619.1. [Q9XVI6-1]
UniGeneiCel.17398.

Genome annotation databases

EnsemblMetazoaiT22G5.5a.1; T22G5.5a.1; WBGene00011932. [Q9XVI6-1]
T22G5.5a.2; T22G5.5a.2; WBGene00011932. [Q9XVI6-1]
GeneIDi179884.
KEGGicel:CELE_T22G5.5.
UCSCiT22G5.5.1. c. elegans. [Q9XVI6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81127 Genomic DNA. Translation: CAB03390.2.
Z81127 Genomic DNA. Translation: CCG28222.1.
PIRiT25126.
RefSeqiNP_001256547.1. NM_001269618.1. [Q9XVI6-2]
NP_001256548.1. NM_001269619.1. [Q9XVI6-1]
UniGeneiCel.17398.

3D structure databases

ProteinModelPortaliQ9XVI6.
SMRiQ9XVI6. Positions 133-502.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-26788N.
IntActiQ9XVI6. 1 interaction.
MINTiMINT-1127619.
STRINGi6239.T22G5.5.1.

Proteomic databases

PaxDbiQ9XVI6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiT22G5.5a.1; T22G5.5a.1; WBGene00011932. [Q9XVI6-1]
T22G5.5a.2; T22G5.5a.2; WBGene00011932. [Q9XVI6-1]
GeneIDi179884.
KEGGicel:CELE_T22G5.5.
UCSCiT22G5.5.1. c. elegans. [Q9XVI6-1]

Organism-specific databases

CTDi179884.
WormBaseiT22G5.5a; CE31996; WBGene00011932; sptl-3.
T22G5.5b; CE47328; WBGene00011932; sptl-3.

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
InParanoidiQ9XVI6.
OMAiIRRYSAG.
PhylomeDBiQ9XVI6.

Enzyme and pathway databases

UniPathwayiUPA00222.
ReactomeiREACT_183003. Sphingolipid de novo biosynthesis.

Miscellaneous databases

NextBioi907264.
PROiQ9XVI6.

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...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
    Strain: Bristol N2.
  2. "Apicobasal domain identities of expanding tubular membranes depend on glycosphingolipid biosynthesis."
    Zhang H., Abraham N., Khan L.A., Hall D.H., Fleming J.T., Gobel V.
    Nat. Cell Biol. 13:1189-1201(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiSPTC3_CAEEL
AccessioniPrimary (citable) accession number: Q9XVI6
Secondary accession number(s): H9G307
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2013
Last sequence update: March 1, 2003
Last modified: January 7, 2015
This is version 108 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.