Gene/Proteome Database (LMPD)

LMPD ID
LMP001176
Gene ID
10558
Species
Homo sapiens (Human)
Gene Name
serine palmitoyltransferase, long chain base subunit 1
Gene Symbol
SPTLC1
Synonyms
HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI
Alternate Names
serine palmitoyltransferase 1; LCB 1; SPT 1; serine C-palmitoyltransferase; serine-palmitoyl-CoA transferase 1; long chain base biosynthesis protein 1
Chromosome
9
Map Location
9q22.2
EC Number
2.3.1.50
Summary
This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
Orthologs
View orthologs and multiple alignments for SPTLC1

Proteins

serine palmitoyltransferase 1 isoform a
Refseq ID NP_006406
Protein GI 5454084
UniProt ID O15269
mRNA ID NM_006415
Length 473
RefSeq Status REVIEWED
MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVGESLSPAFHLQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL
serine palmitoyltransferase 1 isoform b
Refseq ID NP_847894
Protein GI 30474871
UniProt ID O15269
mRNA ID NM_178324
Length 143
RefSeq Status REVIEWED
MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE
serine palmitoyltransferase 1 isoform c
Refseq ID NP_001268232
Protein GI 526252798
UniProt ID O15269
mRNA ID NM_001281303
Length 513
RefSeq Status REVIEWED
MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVGESLSPAFHLQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPRGRTGESCVHHQGGSPGRPALGRVPGPWPPATQHAERTQDSRWPWSGLKESKNMWIFDRIVTKWCQYGPIV

Gene Information

Entrez Gene ID
10558
Gene Name
serine palmitoyltransferase, long chain base subunit 1
Gene Symbol
SPTLC1
Species
Homo sapiens

Gene Ontology (GO Annotations)

GO ID Source Type Description
GO:0035339 IDA:UniProtKB C SPOTS complex
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:0046513 IEA:Ensembl P ceramide biosynthetic process
GO:0044281 TAS:Reactome P small molecule metabolic process
GO:0046511 IEA:Ensembl P sphinganine biosynthetic process
GO:0030148 TAS:UniProtKB P sphingolipid biosynthetic process
GO:0006665 TAS:Reactome P sphingolipid metabolic process
GO:0006686 IEA:Ensembl P sphingomyelin biosynthetic process
GO:0046512 IEA:Ensembl P sphingosine biosynthetic process

BIOCYC Pathway Links

BIOCYC Pathway ID Description
PWY3DJ-12 ceramide biosynthesis

REACTOME Pathway Links

REACTOME Pathway ID Description
REACT_115810 Sphingolipid de novo biosynthesis

Domain Information

InterPro Annotations

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

UniProt Annotations

Entry Information

Gene Name
serine palmitoyltransferase, long chain base subunit 1
Protein Entry
SPTC1_HUMAN
UniProt ID
O15269
Species
Human

Comments

Comment Type Description
Alternative Products Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O15269-1; Sequence=Displayed; Name=2; IsoId=O15269-2; Sequence=VSP_043127, VSP_043128; Note=No experimental confirmation available.;
Biophysicochemical Properties Kinetic parameters: KM=0.75 mM for serine ; Vmax=1350 pmol/min/mg enzyme ;
Catalytic Activity Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D- sphinganine + CO(2).
Caution Variant Ala-387 has been originally thought to cause HSAN1A (PubMed:15037712). Subsequently, it has been shown to be a rare, benign polymorphism found in homozygous state in a healthy individual (PubMed:19132419). {ECO
Cofactor Name=pyridoxal 5'-phosphate; Xref=ChEBI
Disease Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A) [MIM
Function Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1- SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference.
Pathway Lipid metabolism; sphingolipid metabolism.
Ptm Phosphorylation at Tyr-164 inhibits activity and promotes cell survival.
Similarity Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
Subcellular Location Endoplasmic reticulum membrane {ECO
Subunit Heterodimer with SPTLC2 or SPTLC3. Component of the serine palmitoyltransferase (SPT) complex, composed of SPTLC1, either SPTLC2 or SPTLC3, and either SPTSSA or SPTSSB. Interacts with SPTSSA and SPTSSB; the interaction is direct. Interacts with ORMDL3. {ECO
Tissue Specificity Widely expressed. Not detected in small intestine.

Identical and Related Proteins

Unique RefSeq proteins for LMP001176 (as displayed in Record Overview)

Protein GI Database Accession Length Protein Name
5454084 RefSeq NP_006406 473 serine palmitoyltransferase 1 isoform a
30474871 RefSeq NP_847894 143 serine palmitoyltransferase 1 isoform b
526252798 RefSeq NP_001268232 513 serine palmitoyltransferase 1 isoform c

Identical Sequences to LMP001176 proteins

Reference Database Accession Length Protein Name
GI:5454084 DBBJ BAF84235.1 473 unnamed protein product [Homo sapiens]
GI:5454084 GenBank AAK29328.1 473 serine palmitoyltransferase [Homo sapiens]
GI:30474871 GenBank AAH07085.1 143 Serine palmitoyltransferase, long chain base subunit 1 [Homo sapiens]
GI:5454084 GenBank EAW62804.1 473 serine palmitoyltransferase, long chain base subunit 1, isoform CRA_a [Homo sapiens]
GI:5454084 GenBank EAW62805.1 473 serine palmitoyltransferase, long chain base subunit 1, isoform CRA_a [Homo sapiens]
GI:526252798 GenBank EAW62806.1 513 serine palmitoyltransferase, long chain base subunit 1, isoform CRA_b [Homo sapiens]
GI:5454084 GenBank ACM84322.1 473 Sequence 9820 from patent US 6812339
GI:5454084 GenBank AHD80177.1 473 Sequence 31642 from patent US 8586006
GI:30474871 GenBank AHD80178.1 143 Sequence 31643 from patent US 8586006

Related Sequences to LMP001176 proteins

Reference Database Accession Length Protein Name
GI:30474871 DBBJ BAF84235.1 473 unnamed protein product [Homo sapiens]
GI:5454084 DBBJ BAK62056.1 473 serine palmitoyltransferase 1 [Pan troglodytes]
GI:30474871 EMBL CAA69941.1 473 serine palmitoyltransferase, subunit I [Homo sapiens]
GI:526252798 GenBank AAH68537.1 513 SPTLC1 protein [Homo sapiens]
GI:30474871 GenBank EAW62805.1 473 serine palmitoyltransferase, long chain base subunit 1, isoform CRA_a [Homo sapiens]
GI:30474871 GenBank ACM84322.1 473 Sequence 9820 from patent US 6812339
GI:526252798 GenBank AFL44413.1 513 Sequence 5 from patent US 8183005
GI:5454084 GenBank JAA02106.1 473 serine palmitoyltransferase, long chain base subunit 1 [Pan troglodytes]
GI:5454084 GenBank JAA13390.1 473 serine palmitoyltransferase, long chain base subunit 1 [Pan troglodytes]
GI:5454084 GenBank JAA22994.1 473 serine palmitoyltransferase, long chain base subunit 1 [Pan troglodytes]
GI:5454084 GenBank JAA38378.1 473 serine palmitoyltransferase, long chain base subunit 1 [Pan troglodytes]
GI:526252798 GenBank AIC59652.1 513 SPTLC1, partial [synthetic construct]
GI:30474871 RefSeq NP_006406.1 473 serine palmitoyltransferase 1 isoform a [Homo sapiens]
GI:526252798 RefSeq XP_003938246.1 513 PREDICTED: serine palmitoyltransferase 1 isoform X2 [Saimiri boliviensis boliviensis]
GI:5454084 RefSeq NP_001267361.1 473 serine palmitoyltransferase 1 [Pan troglodytes]
GI:526252798 RefSeq XP_005582295.1 479 PREDICTED: uncharacterized LOC101864870 isoform X2 [Macaca fascicularis]
GI:526252798 RefSeq XP_008256154.1 534 PREDICTED: serine palmitoyltransferase 1 isoform X2 [Oryctolagus cuniculus]
GI:30474871 SwissProt O15269.1 473 RecName: Full=Serine palmitoyltransferase 1; AltName: Full=Long chain base biosynthesis protein 1; Short=LCB 1; AltName: Full=Serine-palmitoyl-CoA transferase 1; Short=SPT 1; Short=SPT1 [Homo sapiens]