LIPID MAPS

LMPD ID

LMP012382

Gene ID

55304

Species

Homo sapiens (Human)

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Gene Symbol

SPTLC3

Synonyms

LCB3; SPT3; LCB2B; hLCB2b; SPTLC2L; C20orf38; dJ718P11; dJ718P11.1;

Chromosome

20

Map Location

20p12.1

EC Number

2.3.1.50

Summary

The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 [PubMed 17023427]). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713) or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006 [PubMed 17023427]). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB (MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]

Orthologs

View orthologs and multiple alignments for SPTLC3

serine palmitoyltransferase 3
Refseq ID	NP_060797
Protein GI	119220554
UniProt ID	Q9NUV7
mRNA ID	NM_018327
Length	552
MANPGGGAVCNGKLHNHKKQSNGSQSRNCTKNGIVKEAQQNGKPHFYDKLIVESFEEAPLHVMVFTYMGYGIGTLFGYLRDFLRNWGIEKCNAAVERKEQKDFVPLYQDFENFYTRNLYMRIRDNWNRPICSAPGPLFDLMERVSDDYNWTFRFTGRVIKDVINMGSYNFLGLAAKYDESMRTIKDVLEVYGTGVASTRHEMGTLDKHKELEDLVAKFLNVEAAMVFGMGFATNSMNIPALVGKGCLILSDELNHTSLVLGARLSGATIRIFKHNNTQSLEKLLRDAVIYGQPRTRRAWKKILILVEGVYSMEGSIVHLPQIIALKKKYKAYLYIDEAHSIGAVGPTGRGVTEFFGLDPHEVDVLMGTFTKSFGASGGYIAGRKDLVDYLRVHSHSAVYASSMSPPIAEQIIRSLKLIMGLDGTTQGLQRVQQLAKNTRYFRQRLQEMGFIIYGNENASVVPLLLYMPGKVAAFARHMLEKKIGVVVVGFPATPLAEARARFCVSAAHTREMLDTVLEALDEMGDLLQLKYSRHKKSARPELYDETSFELED

Entrez Gene ID

55304

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Gene Symbol

SPTLC3

Species

Homo sapiens

Gene Ontology (GO Annotations)

GO ID	Source	Type	Description
GO:0005789	TAS:Reactome	C	endoplasmic reticulum membrane
GO:0016021	IEA:UniProtKB-KW	C	integral component of membrane
GO:0017059	IDA:UniProtKB	C	serine C-palmitoyltransferase complex
GO:0030170	IEA:InterPro	F	pyridoxal phosphate binding
GO:0004758	IDA:UniProtKB	F	serine C-palmitoyltransferase activity
GO:0044281	TAS:Reactome	P	small molecule metabolic process
GO:0046520	IDA:MGI	P	sphingoid biosynthetic process
GO:0030148	TAS:UniProtKB	P	sphingolipid biosynthetic process
GO:0006665	TAS:Reactome	P	sphingolipid metabolic process

KEGG Pathway Links

KEGG Pathway ID	Description
M00094	Ceramide biosynthesis
hsa01100	Metabolic pathways
hsa00600	Sphingolipid metabolism
ko00600	Sphingolipid metabolism
M00099	Sphingosine biosynthesis

REACTOME Pathway Links

REACTOME Pathway ID	Description
REACT_111217	Metabolism
REACT_22258	Metabolism of lipids and lipoproteins
REACT_115810	Sphingolipid de novo biosynthesis
REACT_19323	Sphingolipid metabolism

InterPro Annotations

Accession	Description
IPR004839	Aminotransferase, class I/classII
IPR001917	Aminotransferase, class-II, pyridoxal-phosphate binding site
IPR015424	Pyridoxal phosphate-dependent transferase
IPR015421	Pyridoxal phosphate-dependent transferase, major region, subdomain 1
IPR015422	Pyridoxal phosphate-dependent transferase, major region, subdomain 2

Entry Information

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Protein Entry

SPTC3_HUMAN

UniProt ID

Q9NUV7

Species

Human

Comments

Comment Type	Description
Alternative Products	Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9NUV7-1; Sequence=Displayed; Name=2; IsoId=Q9NUV7-2; Sequence=VSP_028167, VSP_028168; Note=Variant in position: 149:P->A (in dbSNP:rs934335).;
Catalytic Activity	Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D- sphinganine + CO(2). {ECO:0000269\|PubMed:17023427, ECO:0000269\|PubMed:19416851}.
Cofactor	Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326; Evidence= ;
Function	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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference
Pathway	Lipid metabolism; sphingolipid metabolism.
Sequence Caution	Sequence=AAH05205.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence= ;
Similarity	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family
Subcellular Location	Endoplasmic reticulum membrane {ECO:0000250}; Single-pass membrane protein
Subunit	Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB)
Tissue Specificity	Expressed in most tissues, except peripheral blood cells and bone marrow, with highest levels in heart, kidney, liver, uterus and skin