Serine C-palmitoyltransferase

serine C-palmitoyltransferase
Identifiers
EC number	2.3.1.50
CAS number	62213-50-7
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / EGO
Search PMC articles PubMed articles NCBI proteins

Serine palmitoyltransferase
Crystallographic structure of serine palmitoyltransferase from S. paucimobilis. The cofactor PLP is visible in the center.[1]
Identifiers
Symbol	SPT1
PDB	2JG2
UniProt	Q93UV0
Other data
EC number	2.3.1.50

serine palmitoyltransferase, long chain base subunit 1
Identifiers
Symbol	SPTLC1
Alt. symbols	HSN1
Entrez	10558
HUGO	11277
OMIM	605712
RefSeq	NM_006415
UniProt	O15269
Other data
EC number	2.3.1.50
Locus	Chr. 9 q22.31

serine palmitoyltransferase, long chain base subunit 2
Identifiers
Symbol	SPTLC2
Entrez	9517
HUGO	11278
OMIM	605713
RefSeq	NM_004863
UniProt	O15270
Other data
EC number	2.3.1.50
Locus	Chr. 14 q24.3

serine palmitoyltransferase, long chain base subunit 3
Identifiers
Symbol	SPTLC3
Alt. symbols	C20orf38, SPTLC2L
Entrez	55304
HUGO	16253
OMIM	611120
RefSeq	NM_018327
UniProt	Q9NUV7
Other data
EC number	2.3.1.50
Locus	Chr. 20 p12.1

In enzymology, a serine C-palmitoyltransferase (EC 2.3.1.50) is an enzyme that catalyzes the chemical reaction:^[2][3]

palmitoyl-CoA + L-serine $\rightleftharpoons$ CoA + 3-dehydro-D-sphinganine + CO₂

Thus, the two substrates of this enzyme are palmitoyl-CoA and L-serine, whereas its 3 products are CoA, 3-dehydro-D-sphinganine, and CO₂.^[4][5] This reaction is a key step in the biosynthesis of sphingosine which is a precursor of many other sphingolipids.^[3]

This enzyme belongs to the family of transferases, specifically those acyltransferases transferring groups other than aminoacyl groups. The systematic name of this enzyme class is palmitoyl-CoA:L-serine C-palmitoyltransferase (decarboxylating). Other names in common use include serine palmitoyltransferase, SPT, 3-oxosphinganine synthetase, and acyl-CoA:serine C-2 acyltransferase decarboxylating. This enzyme participates in sphingolipid metabolism. It employs one cofactor, pyridoxal phosphate.

Structure

Serine C-palmitoyltransferase is a member of the AOS (a-oxoamine synthase) family of PLP-dependent enzymes, which catalyse the condensation of amino acids and acyl-CoA thioester substrates.^[6] The human enzyme is a heterodimer consisting of two monomeric subunits known as long chain base 1 and 2 (LCB1/2) encoded by separate genes.^[1] The active site of LCB2 contains lysine and other key catalytic residues that are not present in LCB1, which does not participate in catalysis but is nevertheless required for the synthesis and stability of the enzyme.^[7]

Key active site residues of serine C-palmitoyltransferase that interact with PLP. Generated from 2JG2.

Mechanism

The PLP (pyridoxal 5′-phosphate)-dependent serine C-palmitoyltransferase carries out the first enzymatic step of de novo sphingolipid biosynthesis. The enzyme catalyses a Claisen-like condensation between L-serine and an acyl-CoA thioester (CoASH) substrate (typically C¹⁶-palmitoyl) or an acyl-ACP (acyl-carrier protein) thioester substrate, to form 3-ketodihydrosphingosine. Initially PLP cofactor is bound to the active-site lysine via a Schiff base to form the holo-form or internal aldimine of the enzyme. The amine group of L-serine then attacks and displaces the lysine bound to PLP, forming the external aldimine intermediate. Subsequently, deprotonation occurs at the Cα of serine, forming the quinonoid intermediate that attacks the incoming thioester substrate. Following decarboxylation and lysine attack, the product 3-ketodihydrosphingosine is released and catalytically active PLP is reform. This condensation reaction forms the sphingoid base or long-chain base found in all subsequent intermediate sphingolipids and complex sphingolipids in the organism.^[3]

Isoforms

A variety of different serine C-palmitoyltransferase isoforms exist across different species. Unlike in eukaryotes, where the enzyme is heterodimeric and membrane bound, bacterial enzymes are homodimers and cytoplasmic. Studies of the isoform of the enzyme found in the Gram-negative bacterium S. paucimobilis were the first to elucidate the structure of the enzyme, revealing that PLP cofactor is held in place by several active site residues including Lys²⁶⁵ and His¹⁵⁹.^[8] Specifically, the S. paucimobilis isoform features an active-site arginine residue (Arg³⁷⁸) that plays a key role in stabilizing the carboxy moiety of the PLP-L-serine external aldimine intermediate. Similar arginine residues in enzyme homologues (Arg³⁷⁰, Arg³⁹⁰) play analogous roles.^[9] Other homologues, such as in Sphingobacterium multivorum, feature the carboxy moiety bound to serine and methionine residues via water in place of arginine.^[10] Certain enzyme homologues, such as in S. multivorum as well as B. stolpii, are found to be associated with the inner cell membrane, thus resembling the eukaryotic enzymes.^[11] The B. stolpii homologue also features substrate inhibition by palmitoyl-CoA, a feature shared by the yeast and mammalian homologues.^[12][13][14]

Disease

HSAN1 (hereditary sensory and autonomic neuropathy type 1) is a genetic disorder caused by mutations in either one of SPTLC1 or SPTLC2, genes encoding the two heterodimeric subunits of the eukaryotic serine C-palmitoyltransferase enzyme.^[15][16][17] These mutations have been shown to alter active site specificity, specifically by enhancing the ability of the enzyme to condense L-alanine with the palmitoyl-CoA substrate.^[18] This is consistent with elevated levels of deoxysphingoid bases formed by the condensation of alanine with palmitoyl-CoA observed in HSAN1 patients.^[19]

Species distribution

Serine C-palmitoyltransferase is expressed in a large number of species from bacteria to humans. The bacterial enzyme is a water-soluble homodimer^[2] whereas in eukaryotes the enzyme is a heterodimer which is anchored to the endoplasmic reticulum.^[3] Humans and other mammals express three paralogous subunits SPTLC1, SPTLC2, and SPTLC3. It was originally proposed that the functional human enzyme is a heterodimer between a SPTLC1 subunit and a second subunit which is either SPTLC2 or SPTLC3.^[20] However more recent data suggest that the enzyme may exist as a larger complex, possibly an octamer, comprising all three subunits.^[21]

Structural studies

As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 2JG2 and 2JGT.^[1]

References

1. Yard, Beverley A.; Carter, Lester G.; Johnson, Kenneth A.; Overton, Ian M.; Dorward, Mark; Liu, Huanting; McMahon, Stephen A.; Oke, Muse; Puech, Daphné (2007-07-27). "The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis". Journal of Molecular Biology 370 (5): 870–886. doi:10.1016/j.jmb.2007.04.086. ISSN 0022-2836. PMID 17559874.
2. Ikushiro H, Hayashi H, Kagamiyama H (April 2003). "Bacterial serine palmitoyltransferase: a water-soluble homodimeric prototype of the eukaryotic enzyme". Biochim. Biophys. Acta 1647 (1-2): 116–20. doi:10.1016/S1570-9639(03)00074-8. PMID 12686119.
3. Hanada K (June 2003). "Serine palmitoyltransferase, a key enzyme of sphingolipid metabolism". Biochim. Biophys. Acta 1632 (1-3): 16–30. doi:10.1016/S1388-1981(03)00059-3. PMID 12782147.
4. Brady RN, Di Mari SJ, Snell EE (January 1969). "Biosynthesis of sphingolipid bases. 3. Isolation and characterization of ketonic intermediates in the synthesis of sphingosine and dihydrosphingosine by cell-free extracts of Hansenula ciferri". J. Biol. Chem. 244 (2): 491–6. PMID 4388074.
5. Stoffel W, LeKim D, Sticht G (May 1968). "Biosynthesis of dihydrosphingosine in vitro". Hoppe-Seyler's Z. Physiol. Chem. 349 (5): 664–70. doi:10.1515/bchm2.1968.349.1.664. PMID 4386961.
6. Eliot, Andrew C.; Kirsch, Jack F. (2004-01-01). "Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations". Annual Review of Biochemistry 73: 383–415. doi:10.1146/annurev.biochem.73.011303.074021. ISSN 0066-4154. PMID 15189147.
7. Han, Gongshe; Gable, Ken; Yan, Lianying; Natarajan, Mukil; Krishnamurthy, Jayasree; Gupta, Sita D.; Borovitskaya, Anna; Harmon, Jeffrey M.; Dunn, Teresa M. (2004-12-17). "The Topology of the Lcb1p Subunit of Yeast Serine Palmitoyltransferase". Journal of Biological Chemistry 279 (51): 53707–53716. doi:10.1074/jbc.M410014200. ISSN 0021-9258. PMID 15485854.
8. Shiraiwa, Yuka; Ikushiro, Hiroko; Hayashi, Hideyuki (2009-06-05). "Multifunctional Role of His159in the Catalytic Reaction of Serine Palmitoyltransferase". Journal of Biological Chemistry 284 (23): 15487–15495. doi:10.1074/jbc.M808916200. ISSN 0021-9258. PMC 2786316. PMID 19346561.
9. Lowther, Jonathan; Charmier, Guillaume; Raman, Marine C.; Ikushiro, Hiroko; Hayashi, Hideyuki; Campopiano, Dominic J. (2011-06-23). "Role of a conserved arginine residue during catalysis in serine palmitoyltransferase". FEBS Letters 585 (12): 1729–1734. doi:10.1016/j.febslet.2011.04.013. ISSN 1873-3468.
10. Ikushiro, Hiroko; Islam, Mohammad Mainul; Okamoto, Akihiro; Hoseki, Jun; Murakawa, Takeshi; Fujii, Shigeru; Miyahara, Ikuko; Hayashi, Hideyuki (2009-10-01). "Structural Insights into the Enzymatic Mechanism of Serine Palmitoyltransferase from Sphingobacterium multivorum". Journal of Biochemistry 146 (4): 549–562. doi:10.1093/jb/mvp100. ISSN 0021-924X. PMID 19564159.
11. Ikushiro, Hiroko; Islam, Mohammad Mainul; Tojo, Hiromasa; Hayashi, Hideyuki (2007-08-01). "Molecular Characterization of Membrane-Associated Soluble Serine Palmitoyltransferases from Sphingobacterium multivorum and Bdellovibrio stolpii". Journal of Bacteriology 189 (15): 5749–5761. doi:10.1128/JB.00194-07. ISSN 0021-9193. PMC 1951810. PMID 17557831.
12. Gable, Ken; Slife, Harry; Bacikova, Dagmar; Monaghan, Erin; Dunn, Teresa M. (2000-03-17). "Tsc3p Is an 80-Amino Acid Protein Associated with Serine Palmitoyltransferase and Required for Optimal Enzyme Activity". Journal of Biological Chemistry 275 (11): 7597–7603. doi:10.1074/jbc.275.11.7597. ISSN 0021-9258. PMID 10713067.
13. Hanada, Kentaro; Hara, Tomoko; Nishijima, Masahiro (2000-03-24). "Purification of the Serine Palmitoyltransferase Complex Responsible for Sphingoid Base Synthesis by Using Affinity Peptide Chromatography Techniques". Journal of Biological Chemistry 275 (12): 8409–8415. doi:10.1074/jbc.275.12.8409. ISSN 0021-9258. PMID 10722674.
14. Lara, Primo N.; Moon, James; Redman, Mary W.; Semrad, Thomas J.; Kelly, Karen; Allen, Jeffrey W.; Gitlitz, Barbara J.; Mack, Philip C.; Gandara, David R. (2015-01-01). "Relevance of platinum sensitivity status in relapsed/refractory extensive stage small cell lung cancer (ES-SCLC) in the modern era: A patient level analysis of SWOG trials". Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 10 (1): 110–115. doi:10.1097/JTO.0000000000000385. ISSN 1556-0864. PMC 4320001. PMID 25490004.
15. Bejaoui, K.; Wu, C.; Scheffler, M. D.; Haan, G.; Ashby, P.; Wu, L.; de Jong, P.; Brown, R. H. (2001-03-01). "SPTLC1 is mutated in hereditary sensory neuropathy, type 1". Nature Genetics 27 (3): 261–262. doi:10.1038/85817. ISSN 1061-4036. PMID 11242106.
16. Gable, Ken; Han, Gongshe; Monaghan, Erin; Bacikova, Dagmar; Natarajan, Mukil; Williams, Robert; Dunn, Teresa M. (2002-03-22). "Mutations in the Yeast LCB1 and LCB2Genes, Including Those Corresponding to the Hereditary Sensory Neuropathy Type I Mutations, Dominantly Inactivate Serine Palmitoyltransferase". Journal of Biological Chemistry 277 (12): 10194–10200. doi:10.1074/jbc.M107873200. ISSN 0021-9258. PMID 11781309.
17. Rotthier, Annelies; Auer-Grumbach, Michaela; Janssens, Katrien; Baets, Jonathan; Penno, Anke; Almeida-Souza, Leonardo; Van Hoof, Kim; Jacobs, An; De Vriendt, Els (2010-10-08). "Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I". American Journal of Human Genetics 87 (4): 513–522. doi:10.1016/j.ajhg.2010.09.010. ISSN 1537-6605. PMC 2948807. PMID 20920666.
18. Gable, Kenneth; Gupta, Sita D.; Han, Gongshe; Niranjanakumari, Somashekarappa; Harmon, Jeffrey M.; Dunn, Teresa M. (2010-07-23). "A Disease-causing Mutation in the Active Site of Serine Palmitoyltransferase Causes Catalytic Promiscuity". Journal of Biological Chemistry 285 (30): 22846–22852. doi:10.1074/jbc.M110.122259. ISSN 0021-9258. PMC 2906276. PMID 20504773.
19. Penno, Anke; Reilly, Mary M.; Houlden, Henry; Laurá, Matilde; Rentsch, Katharina; Niederkofler, Vera; Stoeckli, Esther T.; Nicholson, Garth; Eichler, Florian (2010-04-09). "Hereditary Sensory Neuropathy Type 1 Is Caused by the Accumulation of Two Neurotoxic Sphingolipids". Journal of Biological Chemistry 285 (15): 11178–11187. doi:10.1074/jbc.M109.092973. ISSN 0021-9258. PMC 2856995. PMID 20097765.
20. Hornemann T, Richard S, Rütti MF, Wei Y, von Eckardstein A (December 2006). "Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase". J. Biol. Chem. 281 (49): 37275–81. doi:10.1074/jbc.M608066200. PMID 17023427.
21. Hornemann T, Wei Y, von Eckardstein A (July 2007). "Is the mammalian serine palmitoyltransferase a high-molecular-mass complex?". Biochem. J. 405 (1): 157–64. doi:10.1042/BJ20070025. PMC 1925250. PMID 17331073.