O15269 (SPTC1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Serine palmitoyltransferase 1
EC=2.3.1.50

Alternative name(s):
Long chain base biosynthesis protein 1
Short name=LCB 1
Serine-palmitoyl-CoA transferase 1
Short name=SPT 1
Short name=SPT1

Gene names

Name:	SPTLC1
Synonyms:	LCB1

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	473 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.7
Catalytic activity	Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2. Ref.7
Cofactor	Pyridoxal phosphate By similarity.
Pathway	Lipid metabolism; sphingolipid metabolism.
Subunit structure	Heterodimer with SPTLC2 or SPTLC3. Component of the serine palmitoyltransferase (SPT) complex, composed of SPTLC1, either SPTLC2 or SPTLC3, and either SSSPTA or SSSPTB. Interacts with SPTSSA and SPTSSB; the interaction is direct. Interacts with ORMDL3. Ref.7 Ref.8
Subcellular location	Endoplasmic reticulum membrane; Single-pass membrane protein By similarity.
Tissue specificity	Widely expressed. Not detected in small intestine. Ref.6
Involvement in disease	Defects in SPTLC1 are the cause of hereditary sensory and autonomic neuropathy type 1A (HSAN1A) [MIM:162400]. The hereditary sensory and autonomic neuropathies are a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN1A is an autosomal dominant axonal neuropathy with onset in the second or third decades. Initial symptoms are loss of pain, touch, heat, and cold sensation over the feet, followed by distal muscle wasting and weakness. Loss of pain sensation leads to chronic skin ulcers and distal amputations. Ref.2 Ref.13 Ref.14 Ref.15
Sequence similarities	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
Caution	Variant Ala-387 has been originally thought to cause HSAN1A (Ref.10). Subsequently, it has been shown to be a rare, benign polymorphism found in homozygous state in a healthy individual (Ref.14).

Ontologies

Keywords
Cellular component	Endoplasmic reticulum Membrane
Coding sequence diversity	Polymorphism
Disease	Disease mutation Neuropathy
Domain	Transmembrane Transmembrane helix
Ligand	Pyridoxal phosphate
Molecular function	Acyltransferase Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Cellular component	SPOTS complex Inferred from direct assay Ref.8. Source: UniProtKB integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	protein binding Inferred from physical interaction Ref.7Ref.8. Source: UniProtKB pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro serine C-palmitoyltransferase activity Inferred from direct assay Ref.7. Source: UniProtKB transferase activity, transferring nitrogenous groups Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 473	473	Serine palmitoyltransferase 1		PRO_0000163853
Regions
	Topological domain	1 – 15	15	Lumenal Potential
	Transmembrane	16 – 36	21	Helical; Potential
	Topological domain	37 – 473	437	Cytoplasmic Potential
Natural variations
	Natural variant	133	1	C → W in HSAN1A; reduced activity; does not interfere with SPT complex formation. Ref.2 Ref.14		VAR_011392
	Natural variant	133	1	C → Y in HSAN1A; reduced activity; does not interfere with SPT complex formation. Ref.2 Ref.14		VAR_011393
	Natural variant	144	1	V → D in HSAN1A; reduced activity; does not interfere with SPT complex formation. Ref.2 Ref.14		VAR_011394
	Natural variant	151	1	R → L. Ref.11 Corresponds to variant rs45461899 [ dbSNP | Ensembl ].		VAR_037889
	Natural variant	239	1	R → W in a breast cancer sample; somatic mutation. Ref.12		VAR_036610
	Natural variant	331	1	S → F in HSAN1A; reduced activity. Ref.13 Ref.15		VAR_066245
	Natural variant	352	1	A → V in HSAN1A; reduced activity. Ref.13 Ref.15		VAR_066246
	Natural variant	387	1	G → A Rare polymorphism; does not affect activity; does not interfere with SPT complex formation. Ref.10 Ref.14		VAR_037890

Sequences

	Sequence		Length	Mass (Da)
	O15269 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: BA9E056A869D2EA2	FASTA	473	52,744
	10 20 30 40 50 60 MATATEQWVL VEMVQALYEA PAYHLILEGI LILWIIRLLF SKTYKLQERS DLTVKEKEEL 70 80 90 100 110 120 IEEWQPEPLV PPVPKDHPAL NYNIVSGPPS HKTVVNGKEC INFASFNFLG LLDNPRVKAA 130 140 150 160 170 180 ALASLKKYGV GTCGPRGFYG TFDVHLDLED RLAKFMKTEE AIIYSYGFAT IASAIPAYSK 190 200 210 220 230 240 RGDIVFVDRA ACFAIQKGLQ ASRSDIKLFK HNDMADLERL LKEQEIEDQK NPRKARVTRR 250 260 270 280 290 300 FIVVEGLYMN TGTICPLPEL VKLKYKYKAR IFLEESLSFG VLGEHGRGVT EHYGINIDDI 310 320 330 340 350 360 DLISANMENA LASIGGFCCG RSFVIDHQRL SGQGYCFSAS LPPLLAAAAI EALNIMEENP 370 380 390 400 410 420 GIFAVLKEKC GQIHKALQGI SGLKVVGESL SPAFHLQLEE STGSREQDVR LLQEIVDQCM 430 440 450 460 470 NRSIALTQAR YLEKEEKCLP PPSIRVVVTV EQTEEELERA ASTIKEVAQA VLL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 9363775] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Kidney.
[2]	"Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I." Dawkins J.L., Hulme D.J., Brahmbhatt S.B., Auer-Grumbach M., Nicholson G.A. Nat. Genet. 27:309-312(2001) [PubMed: 11242114] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], VARIANTS HSAN1A TRP-133; TYR-133 AND ASP-144.
[3]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Placenta.
[4]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed: 15164053] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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: 17023427] [Abstract] Cited for: TISSUE SPECIFICITY.
[7]	"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: 19416851] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION IN THE SPT COMPLEX, INTERACTION WITH C3ORF57 AND C14ORF147.
[8]	"Orm family proteins mediate sphingolipid homeostasis." Breslow D.K., Collins S.R., Bodenmiller B., Aebersold R., Simons K., Shevchenko A., Ejsing C.S., Weissman J.S. Nature 463:1048-1053(2010) [PubMed: 20182505] [Abstract] Cited for: INTERACTION WITH ORMDL3.
[9]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"SPTLC1 mutation in twin sisters with hereditary sensory neuropathy type I." Verhoeven K., Coen K., De Vriendt E., Jacobs A., Van Gerwen V., Smouts I., Pou-Serradell A., Martin J.-J., Timmerman V., De Jonghe P. Neurology 62:1001-1002(2004) [PubMed: 15037712] [Abstract] Cited for: VARIANT ALA-387.
[11]	"Charcot-Marie-Tooth disease due to a de novo mutation of the RAB7 gene." Meggouh F., Bienfait H.M.E., Weterman M.A.J., de Visser M., Baas F. Neurology 67:1476-1478(2006) [PubMed: 17060578] [Abstract] Cited for: VARIANT LEU-151.
[12]	"The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. Science 314:268-274(2006) [PubMed: 16959974] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] TRP-239.
[13]	"Genes for hereditary sensory and autonomic neuropathies: a genotype-phenotype correlation." Rotthier A., Baets J., De Vriendt E., Jacobs A., Auer-Grumbach M., Levy N., Bonello-Palot N., Kilic S.S., Weis J., Nascimento A., Swinkels M., Kruyt M.C., Jordanova A., De Jonghe P., Timmerman V. Brain 132:2699-2711(2009) [PubMed: 19651702] [Abstract] Cited for: VARIANTS HSAN1A PHE-331 AND VAL-352.
[14]	"A systematic comparison of all mutations in hereditary sensory neuropathy type I (HSAN I) reveals that the G387A mutation is not disease associated." Hornemann T., Penno A., Richard S., Nicholson G., van Dijk F.S., Rotthier A., Timmerman V., von Eckardstein A. Neurogenetics 10:135-143(2009) [PubMed: 19132419] [Abstract] Cited for: CHARACTERIZATION OF VARIANTS HSAN1A TYR-133; TRP-133 AND ASP-144, CHARACTERIZATION OF VARIANT ALA-387, LACK OF ASSOCIATION OF VARIANT ALA-387 WITH HSAN1A.
[15]	"Characterization of two mutations in the SPTLC1 subunit of serine palmitoyltransferase associated with hereditary sensory and autonomic neuropathy type I." Rotthier A., Penno A., Rautenstrauss B., Auer-Grumbach M., Stettner G.M., Asselbergh B., Van Hoof K., Sticht H., Levy N., Timmerman V., Hornemann T., Janssens K. Hum. Mutat. 32:E2211-E2225(2011) [PubMed: 21618344] [Abstract] Cited for: VARIANT HSAN1A PHE-331, CHARACTERIZATION OF VARIANTS HSAN1A PHE-331 AND VAL-352.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases
EMBL GenBank DDBJ	Y08685 mRNA. Translation: CAA69941.1. AF286717 , AF286703, AF286704, AF286705, AF286706, AF286707, AF286708, AF286709, AF286710, AF286711, AF286712, AF286713, AF286714, AF286715, AF286716 Genomic DNA. Translation: AAK29328.1. AK291546 mRNA. Translation: BAF84235.1. AL391219, AL354751 Genomic DNA. Translation: CAH70209.1. AL354751, AL391219 Genomic DNA. Translation: CAH69924.1. CH471089 Genomic DNA. Translation: EAW62804.1.
IPI	IPI00005745.
RefSeq	NP_006406.1. NM_006415.2.
UniGene	Hs.90458.
3D structure databases
ProteinModelPortal	O15269.
SMR	O15269. Positions 54-471.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-45626N.
IntAct	O15269. 5 interactions.
STRING	O15269.
PTM databases
PhosphoSite	O15269.
Proteomic databases
PeptideAtlas	O15269.
PRIDE	O15269.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000262554; ENSP00000262554; ENSG00000090054.
GeneID	10558.
KEGG	hsa:10558.
UCSC	uc004arl.1. human.
Organism-specific databases
CTD	10558.
GeneCards	GC09M094793.
H-InvDB	HIX0008162.
HGNC	HGNC:11277. SPTLC1.
HPA	CAB018747. HPA010860.
MIM	162400. phenotype. 605712. gene.
neXtProt	NX_O15269.
Orphanet	36386. Hereditary sensory and autonomic neuropathy type 1.
PharmGKB	PA36106.
GenAtlas	Search...
Phylogenomic databases
HOVERGEN	HBG003992.
InParanoid	O15269.
OrthoDB	EOG4XPQFX.
PhylomeDB	O15269.
Enzyme and pathway databases
BRENDA	2.3.1.50. 2681.
Reactome	REACT_22258. Metabolism of lipids and lipoproteins.
Gene expression databases
ArrayExpress	O15269.
Bgee	O15269.
CleanEx	HS_SPTLC1.
Genevestigator	O15269.
GermOnline	ENSG00000090054. Homo sapiens.
Family and domain databases
InterPro	IPR004839. Aminotransferase_I/II. IPR015424. PyrdxlP-dep_Trfase_major_dom. IPR015421. PyrdxlP-dep_Trfase_major_sub1. IPR015422. PyrdxlP-dep_Trfase_major_sub2. [Graphical view]
Gene3D	G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit. G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.
KO	K00654.
Pfam	PF00155. Aminotran_1_2. 1 hit. [Graphical view]
SUPFAM	SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITE	PS00599. AA_TRANSFER_CLASS_2. False negative. [Graphical view]
ProtoNet	Search...
Other
DrugBank	DB00133. L-Serine. DB00114. Pyridoxal Phosphate.
NextBio	40067.
SOURCE	Search...

Entry information

Entry name

SPTC1_HUMAN

Accession

Primary (citable) accession number: O15269
Secondary accession number(s): A8K681, Q5VWB4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 1, 1998
Last modified:	January 25, 2012
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.