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Protein

Serine palmitoyltransferase 2

Gene

SPTLC2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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: MGI
  • sphingomyelin biosynthetic process Source: Ensembl
  • sphingosine biosynthetic process Source: Ensembl

Keywordsi

Molecular functionAcyltransferase, Transferase
Biological processLipid metabolism, Sphingolipid metabolism
LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc: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

EuPathDBiHostDB:ENSG00000100596.6
HGNCiHGNC:11278 SPTLC2
MIMi605713 gene
neXtProtiNX_O15270

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

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 PublicationCorresponds to variant dbSNP:rs864621998Ensembl.1
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 dbSNP:rs267607090Ensembl.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 dbSNP:rs267607089Ensembl.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 dbSNP:rs267607091Ensembl.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
DB00114 Pyridoxal Phosphate

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

BioGridi11489417 interactors.
CORUMiO15270
DIPiDIP-34604N
IntActiO15270 14 interactors.
MINTiO15270
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
OMAiTLNMSSY
OrthoDBiEOG091G0558
PhylomeDBiO15270
TreeFamiTF300452

Family and domain databases

Gene3Di3.40.640.101 hit
3.90.1150.102 hits
InterProiView protein in InterPro
IPR001917 Aminotrans_II_pyridoxalP_BS
IPR004839 Aminotransferase_I/II
IPR015424 PyrdxlP-dep_Trfase
IPR015422 PyrdxlP-dep_Trfase_dom1
IPR015421 PyrdxlP-dep_Trfase_major
PfamiView protein in Pfam
PF00155 Aminotran_1_2, 1 hit
SUPFAMiSSF53383 SSF53383, 1 hit
PROSITEiView protein in PROSITE
PS00599 AA_TRANSFER_CLASS_2, 1 hit

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 PublicationCorresponds to variant dbSNP:rs864621998Ensembl.1
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 dbSNP:rs267607090Ensembl.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 dbSNP:rs267607089Ensembl.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 dbSNP:rs267607091Ensembl.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

Similar proteinsi

Entry informationi

Entry nameiSPTC2_HUMAN
AccessioniPrimary (citable) accession number: O15270
Secondary accession number(s): Q16685
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: March 28, 2018
This is version 167 of the entry and version 1 of the sequence. See 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