Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

O15270

- SPTC2_HUMAN

UniProt

O15270 - SPTC2_HUMAN

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Serine palmitoyltransferase 2

Gene

SPTLC2

Organism
Homo sapiens (Human)
Status
Reviewed - 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

GO - Molecular functioni

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

GO - Biological processi

  1. ceramide biosynthetic process Source: Ensembl
  2. small molecule metabolic process Source: Reactome
  3. sphinganine biosynthetic process Source: Ensembl
  4. sphingolipid biosynthetic process Source: UniProtKB
  5. sphingolipid metabolic process Source: Reactome
  6. sphingomyelin biosynthetic process Source: Ensembl
  7. 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.
BRENDAi2.3.1.50. 2681.
ReactomeiREACT_115810. 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
ProteomesiUP000005640: Chromosome 14

Organism-specific databases

HGNCiHGNC:11278. SPTLC2.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei67 – 8721HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. endoplasmic reticulum membrane Source: Reactome
  2. integral component of membrane Source: UniProtKB-KW
  3. mitochondrion Source: Ensembl
  4. serine C-palmitoyltransferase complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C) [MIM:613640]: A 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.2 Publications
Note: 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
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti182 – 1821A → P in HSAN1C; reduced activity with L-serine as substrate; increased activity toward L-alanine resulting in the accumulation of 1-deoxy-sphinganine. 1 Publication
VAR_069525
Natural varianti359 – 3591V → 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 Publication
VAR_064798
Natural varianti382 – 3821G → 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 Publication
VAR_064799
Natural varianti504 – 5041I → 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 Publication
VAR_064800

Keywords - Diseasei

Disease mutation, Neuropathy

Organism-specific databases

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 562562Serine palmitoyltransferase 2PRO_0000163858Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei379 – 3791N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

MaxQBiO15270.
PaxDbiO15270.
PeptideAtlasiO15270.
PRIDEiO15270.

PTM databases

PhosphoSiteiO15270.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiO15270.
CleanExiHS_SPTLC2.
ExpressionAtlasiO15270. baseline and differential.
GenevestigatoriO15270.

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. 8 interactions.
DIPiDIP-34604N.
IntActiO15270. 4 interactions.
STRINGi9606.ENSP00000216484.

Structurei

3D structure databases

ProteinModelPortaliO15270.
SMRiO15270. Positions 170-535.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074678.
HOGENOMiHOG000206826.
HOVERGENiHBG002230.
InParanoidiO15270.
KOiK00654.
OMAiPEPGGCC.
OrthoDBiEOG73RBB0.
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 BAA25452.2 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti61 – 644EAFE → TLAR in AAC50871. (PubMed:8921873)Curated
Sequence conflicti436 – 46934KECVQ…DSPVV → NGITIHEVVQTRNTYHRFSP LSPVFSHQCLWIML(PubMed:8921873)CuratedAdd
BLAST

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti182 – 1821A → P in HSAN1C; reduced activity with L-serine as substrate; increased activity toward L-alanine resulting in the accumulation of 1-deoxy-sphinganine. 1 Publication
VAR_069525
Natural varianti359 – 3591V → 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 Publication
VAR_064798
Natural varianti382 – 3821G → 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 Publication
VAR_064799
Natural varianti504 – 5041I → 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 Publication
VAR_064800

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.3. 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 .
CCDSi CCDS9865.1.
PIRi I38873.
RefSeqi NP_004854.1. NM_004863.3.
UniGenei Hs.435661.

3D structure databases

ProteinModelPortali O15270.
SMRi O15270. Positions 170-535.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 114894. 8 interactions.
DIPi DIP-34604N.
IntActi O15270. 4 interactions.
STRINGi 9606.ENSP00000216484.

Chemistry

BindingDBi O15270.
ChEMBLi CHEMBL1250344.
DrugBanki DB00133. L-Serine.
GuidetoPHARMACOLOGYi 2510.

PTM databases

PhosphoSitei O15270.

Proteomic databases

MaxQBi O15270.
PaxDbi O15270.
PeptideAtlasi O15270.
PRIDEi O15270.

Protocols and materials databases

DNASUi 9517.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000216484 ; ENSP00000216484 ; ENSG00000100596 .
GeneIDi 9517.
KEGGi hsa:9517.
UCSCi uc001xub.3. human.

Organism-specific databases

CTDi 9517.
GeneCardsi GC14M077973.
HGNCi HGNC:11278. SPTLC2.
HPAi HPA027552.
MIMi 605713. gene.
613640. phenotype.
neXtProti NX_O15270.
Orphaneti 36386. Hereditary sensory and autonomic neuropathy type 1.
PharmGKBi PA36107.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0156.
GeneTreei ENSGT00550000074678.
HOGENOMi HOG000206826.
HOVERGENi HBG002230.
InParanoidi O15270.
KOi K00654.
OMAi PEPGGCC.
OrthoDBi EOG73RBB0.
PhylomeDBi O15270.
TreeFami TF300452.

Enzyme and pathway databases

UniPathwayi UPA00222 .
BioCyci MetaCyc:HS02117-MONOMER.
BRENDAi 2.3.1.50. 2681.
Reactomei REACT_115810. Sphingolipid de novo biosynthesis.

Miscellaneous databases

ChiTaRSi SPTLC2. human.
GeneWikii SPTLC2.
GenomeRNAii 9517.
NextBioi 35666.
PROi O15270.
SOURCEi Search...

Gene expression databases

Bgeei O15270.
CleanExi HS_SPTLC2.
ExpressionAtlasi O15270. baseline and differential.
Genevestigatori O15270.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProi IPR001917. 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 ]
Pfami PF00155. Aminotran_1_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
PROSITEi PS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Human and murine serine-palmitoyl-CoA transferase. Cloning, expression and characterization of the key enzyme in sphingolipid synthesis."
    Weiss B., Stoffel W.
    Eur. J. Biochem. 249:239-247(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Pancreas.
  2. "Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro."
    Nagase T., Ishikawa K., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 5:31-39(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  3. "The DNA sequence and analysis of human chromosome 14."
    Heilig R., Eckenberg R., Petit J.-L., Fonknechten N., Da Silva C., Cattolico L., Levy M., Barbe V., De Berardinis V., Ureta-Vidal A., Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S., Sun H., Du H.
    , Pepin K., Artiguenave F., Robert C., Cruaud C., Bruels T., Jaillon O., Friedlander L., Samson G., Brottier P., Cure S., Segurens B., Aniere F., Samain S., Crespeau H., Abbasi N., Aiach N., Boscus D., Dickhoff R., Dors M., Dubois I., Friedman C., Gouyvenoux M., James R., Madan A., Mairey-Estrada B., Mangenot S., Martins N., Menard M., Oztas S., Ratcliffe A., Shaffer T., Trask B., Vacherie B., Bellemere C., Belser C., Besnard-Gonnet M., Bartol-Mavel D., Boutard M., Briez-Silla S., Combette S., Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C., Muselet D., Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P., Trybou A., Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M., Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V., Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L., Verdier J., Verdier-Discala C., Hillier L.W., Fulton L., McPherson J., Matsuda F., Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W., Quetier F., Waterston R., Hood L., Weissenbach J.
    Nature 421:601-607(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lymph.
  5. "Sphingolipid synthesis: identification and characterization of mammalian cDNAs encoding the Lcb2 subunit of serine palmitoyltransferase."
    Nagiec M.M., Lester R.L., Dickson R.C.
    Gene 177:237-241(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-470.
    Tissue: Pancreatic islet.
  6. "A molecular inventory of human pancreatic islets: sequence analysis of 1000 cDNA clones."
    Takeda J., Yano H., Eng S., Zeng Y., Bell G.I.
    Hum. Mol. Genet. 2:1793-1798(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 68-144.
    Tissue: Pancreatic islet.
  7. "Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase."
    Hornemann T., Richard S., Ruetti M.F., Wei Y., von Eckardstein A.
    J. Biol. Chem. 281:37275-37281(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  8. "Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities."
    Han G., Gupta S.D., Gable K., Niranjanakumari S., Moitra P., Eichler F., Brown R.H. Jr., Harmon J.M., Dunn T.M.
    Proc. Natl. Acad. Sci. U.S.A. 106:8186-8191(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION IN THE SPT COMPLEX.
  9. Cited for: FUNCTION, VARIANTS HSAN1C MET-359; VAL-382 AND PHE-504, CHARACTERIZATION OF VARIANTS HSAN1C MET-359; VAL-382 AND PHE-504.
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Hereditary sensory and autonomic neuropathy type 1 (HSANI) caused by a novel mutation in SPTLC2."
    Murphy S.M., Ernst D., Wei Y., Laura M., Liu Y.T., Polke J., Blake J., Winer J., Houlden H., Hornemann T., Reilly M.M.
    Neurology 80:2106-2111(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT HSAN1C PRO-182, CHARACTERIZATION OF VARIANT HSAN1C PRO-182, PATHOLOGICAL MECHANISM.

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 26, 2014
This is version 138 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

External Data

Dasty 3