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Protein

Serine palmitoyltransferase 2

Gene

SPTLC2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.2 Publications

Catalytic activityi

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.1 Publication

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: UniProtKB

GO - Biological processi

  • ceramide biosynthetic process Source: MGI
  • positive regulation of lipophagy Source: MGI
  • sphinganine biosynthetic process Source: Ensembl
  • sphingolipid biosynthetic process Source: UniProtKB
  • sphingomyelin biosynthetic process Source: Ensembl
  • sphingosine biosynthetic process Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:HS02117-MONOMER.
ZFISH:HS02117-MONOMER.
BRENDAi2.3.1.50. 2681.
ReactomeiR-HSA-1660661. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine palmitoyltransferase 2 (EC:2.3.1.50)
Alternative name(s):
Long chain base biosynthesis protein 2
Short name:
LCB 2
Long chain base biosynthesis protein 2a
Short name:
LCB2a
Serine-palmitoyl-CoA transferase 2
Short name:
SPT 2
Gene namesi
Name:SPTLC2
Synonyms:KIAA0526, LCB2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:11278. SPTLC2.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei67 – 87HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C)2 Publications
The disease is caused by mutations affecting the gene represented in this entry. SPTLC2 disease mutations cause a shift in the substrate specificity of SPT resulting in the alternative use of L-alanine and L-glycine over its canonical substrate L-serine. This leads to the production of 1-deoxysphingolipids that cannot be correctly metabolized (PubMed:23658386).1 Publication
Disease descriptionA form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by prominent sensory abnormalities with a variable degree of motor and autonomic dysfunction. The neurological phenotype is often complicated by severe infections, osteomyelitis, and amputations. HSAN1C symptoms include loss of touch and vibration in the feet, dysesthesia and severe panmodal sensory loss in the upper and lower limbs, distal lower limb sensory loss with ulceration and osteomyelitis, and distal muscle weakness.
See also OMIM:613640
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_069525182A → P in HSAN1C; reduced activity with L-serine as substrate; increased activity toward L-alanine resulting in the accumulation of 1-deoxy-sphinganine. 1 Publication1
Natural variantiVAR_064798359V → M in HSAN1C; partial loss of normal activity as measured by reduced formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. 1 PublicationCorresponds to variant rs267607090dbSNPEnsembl.1
Natural variantiVAR_064799382G → V in HSAN1C; complete loss of normal activity as measured by lack of formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. 1 PublicationCorresponds to variant rs267607089dbSNPEnsembl.1
Natural variantiVAR_064800504I → F in HSAN1C; partial loss of normal activity as measured by reduced formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. 1 PublicationCorresponds to variant rs267607091dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Neuropathy

Organism-specific databases

DisGeNETi9517.
MalaCardsiSPTLC2.
MIMi613640. phenotype.
OpenTargetsiENSG00000100596.
Orphaneti36386. Hereditary sensory and autonomic neuropathy type 1.
PharmGKBiPA36107.

Chemistry databases

ChEMBLiCHEMBL1250344.
DrugBankiDB00133. L-Serine.

Polymorphism and mutation databases

BioMutaiSPTLC2.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001638581 – 562Serine palmitoyltransferase 2Add BLAST562

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei379N6-(pyridoxal phosphate)lysineBy similarity1

Proteomic databases

EPDiO15270.
MaxQBiO15270.
PaxDbiO15270.
PeptideAtlasiO15270.
PRIDEiO15270.

PTM databases

iPTMnetiO15270.
PhosphoSitePlusiO15270.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiENSG00000100596.
CleanExiHS_SPTLC2.
ExpressionAtlasiO15270. baseline and differential.
GenevisibleiO15270. HS.

Organism-specific databases

HPAiHPA027552.

Interactioni

Subunit structurei

Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB).1 Publication

Protein-protein interaction databases

BioGridi114894. 12 interactors.
DIPiDIP-34604N.
IntActiO15270. 9 interactors.
STRINGi9606.ENSP00000216484.

Chemistry databases

BindingDBiO15270.

Structurei

3D structure databases

ProteinModelPortaliO15270.
SMRiO15270.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG1357. Eukaryota.
COG0156. LUCA.
GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
HOVERGENiHBG002230.
InParanoidiO15270.
KOiK00654.
OMAiTGACQEA.
OrthoDBiEOG091G0558.
PhylomeDBiO15270.
TreeFamiTF300452.

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.

O15270-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRPEPGGCCC RRTVRANGCV ANGEVRNGYV RSSAAAAAAA AAGQIHHVTQ
60 70 80 90 100
NGGLYKRPFN EAFEETPMLV AVLTYVGYGV LTLFGYLRDF LRYWRIEKCH
110 120 130 140 150
HATEREEQKD FVSLYQDFEN FYTRNLYMRI RDNWNRPICS VPGARVDIME
160 170 180 190 200
RQSHDYNWSF KYTGNIIKGV INMGSYNYLG FARNTGSCQE AAAKVLEEYG
210 220 230 240 250
AGVCSTRQEI GNLDKHEELE ELVARFLGVE AAMAYGMGFA TNSMNIPALV
260 270 280 290 300
GKGCLILSDE LNHASLVLGA RLSGATIRIF KHNNMQSLEK LLKDAIVYGQ
310 320 330 340 350
PRTRRPWKKI LILVEGIYSM EGSIVRLPEV IALKKKYKAY LYLDEAHSIG
360 370 380 390 400
ALGPTGRGVV EYFGLDPEDV DVMMGTFTKS FGASGGYIGG KKELIDYLRT
410 420 430 440 450
HSHSAVYATS LSPPVVEQII TSMKCIMGQD GTSLGKECVQ QLAENTRYFR
460 470 480 490 500
RRLKEMGFII YGNEDSPVVP LMLYMPAKIG AFGREMLKRN IGVVVVGFPA
510 520 530 540 550
TPIIESRARF CLSAAHTKEI LDTALKEIDE VGDLLQLKYS RHRLVPLLDR
560
PFDETTYEET ED
Length:562
Mass (Da):62,924
Last modified:January 1, 1998 - v1
Checksum:i0C1AA1E233DE36F1
GO

Sequence cautioni

The sequence BAA25452 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti61 – 64EAFE → TLAR in AAC50871 (PubMed:8921873).Curated4
Sequence conflicti436 – 469KECVQ…DSPVV → NGITIHEVVQTRNTYHRFSP LSPVFSHQCLWIML (PubMed:8921873).CuratedAdd BLAST34

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_069525182A → P in HSAN1C; reduced activity with L-serine as substrate; increased activity toward L-alanine resulting in the accumulation of 1-deoxy-sphinganine. 1 Publication1
Natural variantiVAR_064798359V → M in HSAN1C; partial loss of normal activity as measured by reduced formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. 1 PublicationCorresponds to variant rs267607090dbSNPEnsembl.1
Natural variantiVAR_064799382G → V in HSAN1C; complete loss of normal activity as measured by lack of formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. 1 PublicationCorresponds to variant rs267607089dbSNPEnsembl.1
Natural variantiVAR_064800504I → F in HSAN1C; partial loss of normal activity as measured by reduced formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. 1 PublicationCorresponds to variant rs267607091dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08686 mRNA. Translation: CAA69942.1.
AB011098 mRNA. Translation: BAA25452.2. Different initiation.
AF111168 Genomic DNA. Translation: AAD09621.1.
BC005123 mRNA. Translation: AAH05123.1.
U15555 mRNA. Translation: AAC50871.1.
CCDSiCCDS9865.1.
PIRiI38873.
RefSeqiNP_004854.1. NM_004863.3.
UniGeneiHs.435661.

Genome annotation databases

EnsembliENST00000216484; ENSP00000216484; ENSG00000100596.
GeneIDi9517.
KEGGihsa:9517.
UCSCiuc001xub.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08686 mRNA. Translation: CAA69942.1.
AB011098 mRNA. Translation: BAA25452.2. Different initiation.
AF111168 Genomic DNA. Translation: AAD09621.1.
BC005123 mRNA. Translation: AAH05123.1.
U15555 mRNA. Translation: AAC50871.1.
CCDSiCCDS9865.1.
PIRiI38873.
RefSeqiNP_004854.1. NM_004863.3.
UniGeneiHs.435661.

3D structure databases

ProteinModelPortaliO15270.
SMRiO15270.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114894. 12 interactors.
DIPiDIP-34604N.
IntActiO15270. 9 interactors.
STRINGi9606.ENSP00000216484.

Chemistry databases

BindingDBiO15270.
ChEMBLiCHEMBL1250344.
DrugBankiDB00133. L-Serine.

PTM databases

iPTMnetiO15270.
PhosphoSitePlusiO15270.

Polymorphism and mutation databases

BioMutaiSPTLC2.

Proteomic databases

EPDiO15270.
MaxQBiO15270.
PaxDbiO15270.
PeptideAtlasiO15270.
PRIDEiO15270.

Protocols and materials databases

DNASUi9517.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000216484; ENSP00000216484; ENSG00000100596.
GeneIDi9517.
KEGGihsa:9517.
UCSCiuc001xub.4. human.

Organism-specific databases

CTDi9517.
DisGeNETi9517.
GeneCardsiSPTLC2.
HGNCiHGNC:11278. SPTLC2.
HPAiHPA027552.
MalaCardsiSPTLC2.
MIMi605713. gene.
613640. phenotype.
neXtProtiNX_O15270.
OpenTargetsiENSG00000100596.
Orphaneti36386. Hereditary sensory and autonomic neuropathy type 1.
PharmGKBiPA36107.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1357. Eukaryota.
COG0156. LUCA.
GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
HOVERGENiHBG002230.
InParanoidiO15270.
KOiK00654.
OMAiTGACQEA.
OrthoDBiEOG091G0558.
PhylomeDBiO15270.
TreeFamiTF300452.

Enzyme and pathway databases

UniPathwayiUPA00222.
BioCyciMetaCyc:HS02117-MONOMER.
ZFISH:HS02117-MONOMER.
BRENDAi2.3.1.50. 2681.
ReactomeiR-HSA-1660661. Sphingolipid de novo biosynthesis.

Miscellaneous databases

ChiTaRSiSPTLC2. human.
GeneWikiiSPTLC2.
GenomeRNAii9517.
PROiO15270.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000100596.
CleanExiHS_SPTLC2.
ExpressionAtlasiO15270. baseline and differential.
GenevisibleiO15270. HS.

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 nameiSPTC2_HUMAN
AccessioniPrimary (citable) accession number: O15270
Secondary accession number(s): Q16685
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 156 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. SIMILARITY comments
    Index of protein domains and families

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.