Serine palmitoyltransferase 1 (P25045) - Yeast Metabolome Database

Identification

Name

Serine palmitoyltransferase 1

Synonyms

SPT 1
SPT1
Long chain base biosynthesis protein 1

Gene Name

LCB1

Enzyme Class

2.3.1.50

Biological Properties

General Function

Involved in transferase activity, transferring nitrogenous groups

Specific Function

Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine

Cellular Location

Cytoplasm. Endoplasmic reticulum membrane; Multi-pass membrane protein

SMPDB Pathways

Biosynthesis of unsaturated fatty acids	PW002403
Biosynthesis of unsaturated fatty acids (icosanoyl)	PW002434
Biosynthesis of unsaturated fatty acids (stearoyl)	PW002435
Sphingolipid metabolism	PW002479

KEGG Pathways

Biosynthesis of unsaturated fatty acids	ec01040
Sphingolipid metabolism	ec00600

SMPDB Reactions

L-2-amino-3-oxobutanoic acid + Coenzyme A → Acetyl-CoA + Glycine

Palmityl-CoA + L-Serine + hydron Coenzyme A + Carbon dioxide + 3-Dehydrosphinganine

Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Carbon dioxide

KEGG Reactions

Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Carbon dioxide + Coenzyme A

Metabolites

YMDB ID	Name	View
YMDB00016	Glycine	Show
YMDB00045	Coenzyme A	Show
YMDB00112	L-Serine	Show
YMDB00183	3-Dehydrosphinganine	Show
YMDB00301	Palmityl-CoA	Show
YMDB00312	Acetyl-CoA	Show
YMDB00527	palmitoyl-CoA	Show
YMDB00695	L-2-amino-3-oxobutanoic acid	Show
YMDB00862	hydron	Show
YMDB00912	Carbon dioxide	Show

GO Classification

Component
Not Available
Function
binding
transferase activity, transferring nitrogenous groups
cofactor binding
pyridoxal phosphate binding
catalytic activity
transferase activity
Process
metabolic process
biosynthetic process

Gene Properties

Chromosome Location

chromosome 13

Locus

YMR296C

Gene Sequence

>1677 bp ATGGCACACATCCCAGAGGTTTTACCCAAATCAATACCGATTCCGGCATTTATTGTTACC ACCTCATCGTACCTATGGTACTACTTCAATCTGGTGTTGACTCAAATCCCGGGAGGCCAA TTCATCGTTTCGTACATCAAGAAATCGCATCATGACGATCCATACAGGACCACGGTTGAG ATAGGGCTTATTTTATACGGGATCATCTATTACTTGTCCAAGCCACAACAGAAAAAGAGT CTTCAAGCACAGAAGCCCAACCTATCGCCCCAGGAGATTGACGCGCTAATTGAGGACTGG GAGCCCGAGCCTCTAGTCGACCCTTCTGCCACCGATGAGCAATCGTGGAGGGTGGCCAAA ACACCCGTCACCATGGAAATGCCCATTCAGAACCATATTACTATCACCAGAAACAACCTG CAGGAGAAGTATACCAATGTTTTCAATTTGGCCTCGAACAACTTTTTGCAATTGTCCGCT ACGGAGCCCGTGAAAGAAGTGGTCAAGACCACTATCAAGAATTACGGTGTGGGCGCCTGT GGTCCCGCCGGGTTCTACGGTAACCAGGACGTTCATTACACGTTGGAATATGATTTAGCA CAGTTCTTTGGCACCCAAGGTTCCGTTCTGTACGGGCAAGACTTTTGTGCCGCACCCTCT GTTCTGCCTGCTTTCACAAAGCGTGGTGATGTTATCGTGGCAGACGACCAGGTGTCATTA CCAGTGCAAAATGCTCTGCAACTAAGCAGATCCACAGTCTACTACTTCAACCACAACGAT ATGAATTCGCTAGAATGTTTATTAAACGAGTTGACCGAACAGGAGAAACTTGAGAAACTG CCCGCCATTCCAAGAAAATTTATCGTCACTGAGGGTATTTTCCACAACTCGGGCGATTTA GCTCCGTTGCCTGAGTTGACTAAGCTGAAGAACAAGTACAAGTTCAGACTATTTGTTGAC GAAACCTTCTCCATTGGTGTTCTTGGCGCTACGGGCCGTGGGTTGTCAGAGCACTTCAAC ATGGATCGCGCAACTGCCATTGACATTACCGTTGGGTCCATGGCCACCGCGTTGGGGTCC ACCGGTGGTTTTGTCCTGGGTGACAGTGTTATGTGTTTGCACCAGCGTATTGGTTCCAAT GCATATTGTTTTTCTGCCTGTTTGCCGGCTTACACCGTCACATCCGTCTCCAAAGTCTTG AAATTGATGGACTCCAACAACGACGCCGTCCAGACGCTGCAAAAACTATCCAAATCTTTG CATGATTCCTTTGCATCTGACGACTCCTTGCGTTCATACGTAATCGTCACGTCCTCTCCA GTGTCTGCTGTCCTACATCTGCAACTGACTCCCGCATATAGGTCTCGCAAGTTCGGATAC ACCTGCGAACAGCTATTCGAAACCATGTCAGCTTTGCAAAAGAAGTCCCAGACAAACAAA TTCATTGAGCCATACGAAGAGGAGGAAAAATTTCTGCAGTCCATAGTAGATCATGCTCTT ATTAACTACAACGTTCTCATCACAAGAAACACTATTGTTTTAAAACAGGAGACGCTACCA ATTGTCCCTAGCTTGAAAATCTGCTGTAACGCCGCCATGTCCCCAGAGGAACTCAAAAAT GCTTGCGAAAGTGTCAAGCAGTCCATCCTTGCCTGTTGCCAAGAATCTAATAAATAA

Protein Properties

Pfam Domain Function

Aminotran_1_2 (PF00155 )

Protein Residues

558

Protein Molecular Weight

62206.60156

Protein Theoretical pI

6.1

Signalling Regions

None

Transmembrane Regions

50-84
342-371
425-457

Protein Sequence

>Serine palmitoyltransferase 1 MAHIPEVLPKSIPIPAFIVTTSSYLWYYFNLVLTQIPGGQFIVSYIKKSHHDDPYRTTVE IGLILYGIIYYLSKPQQKKSLQAQKPNLSPQEIDALIEDWEPEPLVDPSATDEQSWRVAK TPVTMEMPIQNHITITRNNLQEKYTNVFNLASNNFLQLSATEPVKEVVKTTIKNYGVGAC GPAGFYGNQDVHYTLEYDLAQFFGTQGSVLYGQDFCAAPSVLPAFTKRGDVIVADDQVSL PVQNALQLSRSTVYYFNHNDMNSLECLLNELTEQEKLEKLPAIPRKFIVTEGIFHNSGDL APLPELTKLKNKYKFRLFVDETFSIGVLGATGRGLSEHFNMDRATAIDITVGSMATALGS TGGFVLGDSVMCLHQRIGSNAYCFSACLPAYTVTSVSKVLKLMDSNNDAVQTLQKLSKSL HDSFASDDSLRSYVIVTSSPVSAVLHLQLTPAYRSRKFGYTCEQLFETMSALQKKSQTNK FIEPYEEEEKFLQSIVDHALINYNVLITRNTIVLKQETLPIVPSLKICCNAAMSPEELKN ACESVKQSILACCQESNK

References

External Links

Resource	Link
Saccharomyces Genome Database	LCB1
Uniprot ID	P25045
Uniprot Name	LCB1_YEAST
GenBank Gene ID	AY693052
Genebank Protein ID	51013555

General Reference

Buede, R., Rinker-Schaffer, C., Pinto, W. J., Lester, R. L., Dickson, R. C. (1991). "Cloning and characterization of LCB1, a Saccharomyces gene required for biosynthesis of the long-chain base component of sphingolipids." J Bacteriol 173:4325-4332.2066332
Bowman, S., Churcher, C., Badcock, K., Brown, D., Chillingworth, T., Connor, R., Dedman, K., Devlin, K., Gentles, S., Hamlin, N., Hunt, S., Jagels, K., Lye, G., Moule, S., Odell, C., Pearson, D., Rajandream, M., Rice, P., Skelton, J., Walsh, S., Whitehead, S., Barrell, B. (1997). "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Nature 387:90-93.9169872
Hu, Y., Rolfs, A., Bhullar, B., Murthy, T. V., Zhu, C., Berger, M. F., Camargo, A. A., Kelley, F., McCarron, S., Jepson, D., Richardson, A., Raphael, J., Moreira, D., Taycher, E., Zuo, D., Mohr, S., Kane, M. F., Williamson, J., Simpson, A., Bulyk, M. L., Harlow, E., Marsischky, G., Kolodner, R. D., LaBaer, J. (2007). "Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Genome Res 17:536-543.17322287
Nagiec, M. M., Baltisberger, J. A., Wells, G. B., Lester, R. L., Dickson, R. C. (1994). "The LCB2 gene of Saccharomyces and the related LCB1 gene encode subunits of serine palmitoyltransferase, the initial enzyme in sphingolipid synthesis." Proc Natl Acad Sci U S A 91:7899-7902.8058731
Gable, K., Slife, H., Bacikova, D., Monaghan, E., Dunn, T. M. (2000). "Tsc3p is an 80-amino acid protein associated with serine palmitoyltransferase and required for optimal enzyme activity." J Biol Chem 275:7597-7603.10713067
Gable, K., Han, G., Monaghan, E., Bacikova, D., Natarajan, M., Williams, R., Dunn, T. M. (2002). "Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase." J Biol Chem 277:10194-10200.11781309
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., O'Shea, E. K. (2003). "Global analysis of protein localization in budding yeast." Nature 425:686-691.14562095
Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., Weissman, J. S. (2003). "Global analysis of protein expression in yeast." Nature 425:737-741.14562106
Han, G., Gable, K., Yan, L., Natarajan, M., Krishnamurthy, J., Gupta, S. D., Borovitskaya, A., Harmon, J. M., Dunn, T. M. (2004). "The topology of the Lcb1p subunit of yeast serine palmitoyltransferase." J Biol Chem 279:53707-53716.15485854
Li, X., Gerber, S. A., Rudner, A. D., Beausoleil, S. A., Haas, W., Villen, J., Elias, J. E., Gygi, S. P. (2007). "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." J Proteome Res 6:1190-1197.17330950
Breslow, D. K., Collins, S. R., Bodenmiller, B., Aebersold, R., Simons, K., Shevchenko, A., Ejsing, C. S., Weissman, J. S. (2010). "Orm family proteins mediate sphingolipid homeostasis." Nature 463:1048-1053.20182505