Hmdb loader
Survey
Identification
HMDB Protein ID HMDBP00886
Secondary Accession Numbers
  • 6168
  • HMDBP01711
  • HMDBP04693
Name Serine palmitoyltransferase 1
Synonyms
  1. LCB 1
  2. Long chain base biosynthesis protein 1
  3. SPT 1
  4. SPT1
  5. Serine-palmitoyl-CoA transferase 1
Gene Name SPTLC1
Protein Type Enzyme
Biological Properties
General Function Involved in transferase activity, transferring nitrogenous groups
Specific 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.
Pathways
  • Fabry disease
  • Gaucher Disease
  • Globoid Cell Leukodystrophy
  • Krabbe disease
  • Metachromatic Leukodystrophy (MLD)
  • sphingolipid metabolism
  • Starch and sucrose metabolism
Reactions
Palmityl-CoA + L-Serine → Coenzyme A + 3-Dehydrosphinganine + CO(2) details
Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Coenzyme A + Carbon dioxide details
GO Classification
Biological Process
small molecule metabolic process
phospholipid metabolic process
sphingosine biosynthetic process
sphingolipid biosynthetic process
sphinganine biosynthetic process
sphingomyelin biosynthetic process
Cellular Component
SPOTS complex
integral to membrane
Function
binding
catalytic activity
transferase activity
transferase activity, transferring nitrogenous groups
cofactor binding
pyridoxal phosphate binding
Molecular Function
serine C-palmitoyltransferase activity
pyridoxal phosphate binding
Process
metabolic process
biosynthetic process
Cellular Location
  1. Endoplasmic reticulum membrane
  2. Single-pass membrane protein
Gene Properties
Chromosome Location 9
Locus 9q22.2
SNPs SPTLC1
Gene Sequence
>1422 bp
ATGGCGACCGCCACGGAGCAGTGGGTTCTGGTGGAGATGGTACAGGCGCTTTACGAGGCT
CCTGCTTACCATCTTATTTTGGAAGGGATTCTGATCCTCTGGATAATCAGACTTCTTTTC
TCTAAGACTTACAAATTACAAGAACGATCTGATCTTACAGTCAAGGAAAAAGAAGAACTG
ATTGAAGAGTGGCAACCAGAACCTCTTGTTCCTCCTGTCCCAAAAGACCATCCTGCTCTC
AACTACAACATCGTTTCAGGCCCTCCAAGCCACAAAACTGTGGTGAATGGAAAAGAATGT
ATAAACTTCGCCTCATTTAATTTTCTTGGATTGTTGGATAACCCTAGGGTTAAGGCAGCA
GCTTTAGCATCTCTAAAGAAGTATGGCGTGGGGACTTGTGGACCCAGAGGATTTTATGGC
ACATTTGATGTTCATTTGGATTTGGAAGACCGCCTGGCAAAATTTATGAAGACAGAAGAA
GCCATTATATACTCATATGGATTTGCCACCATAGCCAGTGCTATTCCTGCTTACTCTAAA
AGAGGGGACATTGTTTTTGTAGATAGAGCTGCCTGCTTTGCTATTCAGAAAGGATTACAG
GCATCCCGTAGTGACATTAAGTTATTTAAGCATAATGACATGGCTGACCTCGAGCGACTA
CTAAAAGAACAAGAGATCGAAGATCAAAAGAATCCTCGCAAGGCTCGTGTAACTCGGCGT
TTCATTGTAGTAGAAGGATTGTATATGAATACTGGAACTATTTGTCCTCTTCCAGAATTG
GTTAAGTTAAAATACAAATACAAAGCAAGAATCTTCCTGGAGGAAAGCCTTTCATTTGGA
GTCCTAGGAGAGCATGGCCGAGGAGTCACTGAACACTATGGAATCAATATTGATGATATT
GATCTTATCAGTGCCAACATGGAGAATGCACTTGCTTCTATTGGAGGTTTCTGCTGTGGC
AGGTCTTTTGTAATTGACCATCAGCGACTTTCCGGCCAGGGATACTGCTTTTCAGCTTCG
TTACCTCCCCTGTTAGCTGCTGCAGCAATTGAGGCCCTCAACATCATGGAAGAGAATCCA
GGTATTTTTGCAGTGTTGAAGGAAAAGTGCGGACAAATTCATAAAGCTTTACAAGGCATT
TCTGGATTAAAAGTGGTGGGGGAGTCCCTTTCTCCAGCCTTTCACCTACAACTGGAAGAG
AGCACTGGGTCTCGCGAGCAAGATGTCAGACTGCTTCAGGAAATTGTAGATCAATGCATG
AACAGAAGTATTGCATTAACTCAGGCGCGCTACTTGGAGAAAGAAGAGAAGTGTCTCCCT
CCTCCCAGCATTCGGGTTGTGGTCACGGTGGAACAAACAGAGGAAGAACTGGAGAGAGCT
GCGTCCACCATCAAGGAGGTAGCCCAGGCCGTCCTGCTCTAG
Protein Properties
Number of Residues 473
Molecular Weight 52743.41
Theoretical pI 6.009
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence
>Serine palmitoyltransferase 1
MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEEL
IEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAA
ALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSK
RGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRR
FIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDI
DLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENP
GIFAVLKEKCGQIHKALQGISGLKVVGESLSPAFHLQLEESTGSREQDVRLLQEIVDQCM
NRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL
GenBank ID Protein 2564247
UniProtKB/Swiss-Prot ID O15269
UniProtKB/Swiss-Prot Entry Name SPTC1_HUMAN
PDB IDs Not Available
GenBank Gene ID Y08685
GeneCard ID SPTLC1
GenAtlas ID SPTLC1
HGNC ID HGNC:11277
References
General References
  1. 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 TO, 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: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet. 2004 Jan;36(1):40-5. Epub 2003 Dec 21. [PubMed:14702039 ]
  2. Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RI, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JG, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ES, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blocker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, Dunham I: DNA sequence and analysis of human chromosome 9. Nature. 2004 May 27;429(6990):369-74. [PubMed:15164053 ]
  3. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE: The consensus coding sequences of human breast and colorectal cancers. Science. 2006 Oct 13;314(5797):268-74. Epub 2006 Sep 7. [PubMed:16959974 ]
  4. Weiss B, Stoffel W: Human and murine serine-palmitoyl-CoA transferase--cloning, expression and characterization of the key enzyme in sphingolipid synthesis. Eur J Biochem. 1997 Oct 1;249(1):239-47. [PubMed:9363775 ]
  5. Dawkins JL, Hulme DJ, Brahmbhatt SB, Auer-Grumbach M, Nicholson GA: Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I. Nat Genet. 2001 Mar;27(3):309-12. [PubMed:11242114 ]
  6. Hornemann T, Richard S, Rutti MF, Wei Y, von Eckardstein A: Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase. J Biol Chem. 2006 Dec 8;281(49):37275-81. Epub 2006 Oct 4. [PubMed:17023427 ]
  7. Han G, Gupta SD, Gable K, Niranjanakumari S, Moitra P, Eichler F, Brown RH Jr, Harmon JM, Dunn TM: Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. Proc Natl Acad Sci U S A. 2009 May 19;106(20):8186-91. doi: 10.1073/pnas.0811269106. Epub 2009 May 5. [PubMed:19416851 ]
  8. Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS: Orm family proteins mediate sphingolipid homeostasis. Nature. 2010 Feb 25;463(7284):1048-53. doi: 10.1038/nature08787. [PubMed:20182505 ]
  9. Verhoeven K, Coen K, De Vriendt E, Jacobs A, Van Gerwen V, Smouts I, Pou-Serradell A, Martin JJ, Timmerman V, De Jonghe P: SPTLC1 mutation in twin sisters with hereditary sensory neuropathy type I. Neurology. 2004 Mar 23;62(6):1001-2. [PubMed:15037712 ]
  10. Meggouh F, Bienfait HM, Weterman MA, de Visser M, Baas F: Charcot-Marie-Tooth disease due to a de novo mutation of the RAB7 gene. Neurology. 2006 Oct 24;67(8):1476-8. [PubMed:17060578 ]