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Phytosphingosine (YMDB00285)

Identification
YMDB IDYMDB00285
NamePhytosphingosine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPhytosphingosine (4-hydroxysphinganine) is an intermediate in sphingolipid metabolism pathway. Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannosyl-diinositol-phosphorylceramide (M(IP)2C). Sphingolipid long chain bases (LCBs) - dihydrosphingosine (DHS) and phytosphingosine (PHS) - are implicated as secondary messengers in vital signaling pathways. [Biocyc SPHINGOLIPID-SYN-PWY]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (+)-D-ribo-Phytosphingosine
  • [2S-(2R*,3R*,4S*)]-2-amino-1,3,4-Octadecanetriol
  • 4-D-hydroxy-Sphinganine
  • 4-D-Hydroxysphinganine
  • 4D-Hydroxysphinganine
  • C18-Phytosphingosine
  • D-ribo-1,3,4-Trihydroxy-2-aminooctadecane
  • D-ribo-2-amino-1,3,4-Octadecanetriol
  • 4-R-Hydroxyoctadecasphinganine
  • 8-(Z-e)-C18-Phytosphingenine
  • (2S,3S,4R)-2-Amino-1,3,4-octadecanetriol
  • (2S,3S,4R)-2-Amino-1,3,4-trihydroxyoctadecane
  • D-Ribo-phytosphingosine
  • SP(t18:0)
  • Phytosphingosine
CAS number554-62-1
WeightAverage: 317.5072
Monoisotopic: 317.292994119
InChI KeyAERBNCYCJBRYDG-KSZLIROESA-N
InChIInChI=1S/C18H39NO3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(21)18(22)16(19)15-20/h16-18,20-22H,2-15,19H2,1H3/t16-,17+,18-/m0/s1
IUPAC Name(2S,3S,4R)-2-aminooctadecane-1,3,4-triol
Traditional IUPAC Namephytosphingosine
Chemical FormulaC18H39NO3
SMILES[H]OC([H])([H])[C@]([H])(N([H])[H])[C@]([H])(O[H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as 1,3-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C3 atom.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct Parent1,3-aminoalcohols
Alternative Parents
Substituents
  • 1,3-aminoalcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Polyol
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Primary aliphatic amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point102-103 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.045 g/LALOGPS
logP3.96ALOGPS
logP3.7ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)13.45ChemAxon
pKa (Strongest Basic)8.91ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area86.71 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity92.29 m³·mol⁻¹ChemAxon
Polarizability41.05 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • endoplasmic reticulum
Organoleptic PropertiesNot Available
SMPDB Pathways
Biosynthesis of unsaturated fatty acidsPW002403 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (docosanoyl)PW002408 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (icosanoyl)PW002434 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (stearoyl)PW002435 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)PW002404 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Biosynthesis of unsaturated fatty acidsec01040 Map01040
Sphingolipid metabolismec00600 Map00600
SMPDB Reactions
hydron + oxygen + ferrocytochrome b5 + Sphinganine → water + Phytosphingosine + ferricytochrome b5
Phytosphingosine + hexacosanoyl-CoA → hydron + Coenzyme A + N-hexacosanoyl-C20-4-hydroxysphinganine
Phytosphingosine + Tetracosanoyl-CoA → hydron + Coenzyme A + N-Tetracosanoylphytosphingosine
Phytosphingosine + Docosanoyl-CoA → hydron + Coenzyme A + Cer 18:0;3/22:0;0
stearoyl-CoA + Phytosphingosine → Coenzyme A + hydron + N-stearoylphytosphingosine
KEGG Reactions
Phytosphingosine + Tetracosanoyl-CoA → N-Tetracosanoylphytosphingosine + hydron + Coenzyme A
Phytosphingosine + hexacosanoyl-CoA → N-Hexacosanoylphytosphingosine + hydron + Coenzyme A
Sphinganine + NADPH + hydron + oxygen → NADP + Phytosphingosine + water
Phytosphingosine 1-phosphate + water → Phytosphingosine + phosphate
Adenosine triphosphate + Phytosphingosine → Phytosphingosine 1-phosphate + hydron + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001i-1910000000-6a156f8b67eb8d2e2af8JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0590000000-55f1259ff17447451d03JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001i-1910000000-6a156f8b67eb8d2e2af8JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0590000000-55f1259ff17447451d03JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-08fu-9240000000-f0c822bc0197665bc676JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0pxr-8498250000-59c3446ba7cde2700251JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-03di-9025000000-41591a03203ebe6783abJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, positivesplash10-03yi-9055000000-c534f58f04d1f008079fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, positivesplash10-014i-0009000000-2467642b22875f4e99a1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 7V, positivesplash10-014i-0009000000-94b30bf1ae7ab25e566eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 12V, positivesplash10-03xr-9037000000-2e7ea43f8d534e10f1d4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 15V, positivesplash10-03di-9020000000-ac9c04a9082abb540f22JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 19V, positivesplash10-03di-9010000000-e1fe657c8693bf3f19e7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 26V, positivesplash10-03di-9000000000-f71f3038d0b8478d679cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 31V, positivesplash10-03di-9000000000-795a4947f722e8f61620JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 38V, positivesplash10-03di-9000000000-e62d8c5bcb55aa166603JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 44V, positivesplash10-03di-9000000000-cb05f289ecdcd16de4e7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 52V, positivesplash10-03di-9000000000-e898ac84341e318b5862JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 60V, positivesplash10-08fr-9000000000-b048fe168eacee259394JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 72V, positivesplash10-0900-9000000000-d72ddb3ba2da45266fabJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 22V, positivesplash10-0udi-0039000000-33d42068332d814a2c83JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 22V, positivesplash10-06yt-6940000000-fdeb46044349d9fcc996JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 22V, positivesplash10-0006-9000000000-981a59d4f1dd5e03c5acJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 22V, positivesplash10-0ik9-0190000000-d31bcfd06b73972a4300JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 22V, positivesplash10-03di-2290000000-b7855c3c2203ca25bab3JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uxr-1029000000-ea43e68bb4fffc9657b1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-9121000000-cce64d1dcf28012d72f8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9520000000-d95a37794c98d95dd2b0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-2097000000-1f5b8c8eefe1a491d0c9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bt9-9060000000-7550c32b4e1dfcbc4593JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9020000000-5cbe1fbb421cacd42e98JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Dickson, R. C., Sumanasekera, C., Lester, R. L. (2006). "Functions and metabolism of sphingolipids in Saccharomyces cerevisiae." Prog Lipid Res 45:447-465.16730802
  • Mao, C., Xu, R., Bielawska, A., Szulc, Z. M., Obeid, L. M. (2000). "Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide." J Biol Chem 275:31369-31378.10900202
  • Jiang, J. C., Kirchman, P. A., Zagulski, M., Hunt, J., Jazwinski, S. M. (1998). "Homologs of the yeast longevity gene LAG1 in Caenorhabditis elegans and human." Genome Res 8:1259-1272.9872981
  • Obeid, L. M., Okamoto, Y., Mao, C. (2002). "Yeast sphingolipids: metabolism and biology." Biochim Biophys Acta 1585:163-171.12531550
Synthesis Reference:Mulzer, Johann; Brand, Clemens. Enantioselective syntheses of D- and L-ribo- and arabino-C18-phytosphingosine from (R)-2,3-O-isopropylideneglyceraldehyde. Tetrahedron (1986), 42(21), 5961-8.
External Links:
ResourceLink
CHEBI ID46961
HMDB IDHMDB04610
Pubchem Compound ID122121
Kegg IDC12144
ChemSpider ID108921
FOODB IDFDB023381
Wikipedia IDPhytosphingosine
BioCyc IDPHYTOSPINGOSINE

Enzymes

Protein Details
1. Alkaline ceramidase YDC1
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Specific function:
Catalyzes the conversion of dihydroceramide and also phytoceramide to dihydrosphingosine or phytosphingosine. Prefers dihydroceramide. Very low reverse hydrolysis activity, catalyzing synthesis of dihydroceramide from fatty acid and dihydrosphingosine. Is not responsible for the breakdown of unsaturated ceramide. May play a role in heat stress response
Gene Name:
YDC1
Uniprot ID:
Q02896
Molecular weight:
37230.5
Reactions
Protein Details
2. Sphingosine N-acyltransferase LAG1
General function:
Involved in protein binding
Specific function:
Component of the ceramide synthase complex required for C26-CoA-dependent ceramide synthesis. Redundant with LAC1. Facilitates ER-to-Golgi transport of GPI-anchored proteins. Involved in the aging process. Deletion of LAG1 results in a pronounced increase (approximately 50%) in mean and in maximum life span
Gene Name:
LAG1
Uniprot ID:
P38703
Molecular weight:
48454.10156
Reactions
Acyl-CoA + sphingosine → CoA + N-acylsphingosine.
Protein Details
3. Alkaline ceramidase YPC1
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Specific function:
Hydrolyzes phytoceramide and also dihydroceramide into phytosphingosine or dihydrosphingosine. Prefers phytoceramide. Has also reverse hydrolysis activity, catalyzing synthesis of phytoceramide and dihydroceramide from palmitic acid and phytosphingosine or dihydrosphingosine. Is not responsible for the breakdown of unsaturated ceramide
Gene Name:
YPC1
Uniprot ID:
P38298
Molecular weight:
36419.39844
Reactions
Protein Details
4. Sphingosine N-acyltransferase LAC1
General function:
Involved in identical protein binding
Specific function:
Component of the ceramide synthase complex required for C26-CoA-dependent ceramide synthesis. Redundant with LAG1. Facilitates ER-to-Golgi transport of GPI-anchored proteins
Gene Name:
LAC1
Uniprot ID:
P28496
Molecular weight:
48991.60156
Reactions
Acyl-CoA + sphingosine → CoA + N-acylsphingosine.
Protein Details
5. Sphingoid long chain base kinase 4
General function:
Involved in diacylglycerol kinase activity
Specific function:
Catalyzes the phosphorylation of the sphingoid long chain bases dihydrosphingosine (DHS or sphinganine) and phytosphingosine (PHS) to form dihydrosphingosine 1-phosphate (DHS-1P) and phytosphingosine 1-phosphate (PHS-1P) respectively. Involved in the biosynthesis of sphingolipids and ceramides. Required with LCB3 for an effective incorporation of DHS into ceramides through a phosphorylation-dephosphorylation cycle. Involved in heat-induced transient cell cycle arrest. Accumulation of phosphorylated sphingoid long chain bases (LCBPs) stimulates calcium influx and activates calcineurin signaling. Involved in heat-stress resistance
Gene Name:
LCB4
Uniprot ID:
Q12246
Molecular weight:
69638.60156
Reactions
ATP + sphinganine → ADP + sphinganine 1-phosphate.
ATP + phytosphingosine → ADP + phytosphingosine 1-phosphate.
Protein Details
6. Sphingoid long chain base kinase 5
General function:
Involved in diacylglycerol kinase activity
Specific function:
Catalyzes the phosphorylation of the sphingoid long chain bases dihydrosphingosine (DHS or sphinganine) and phytosphingosine (PHS) to form dihydrosphingosine 1-phosphate (DHS-1P) and phytosphingosine 1-phosphate (PHS-1P) respectively. Redundant to LCB4, is only responsible for few percent of the total activity. Involved in the biosynthesis of sphingolipids and ceramides. Involved in heat-induced transient cell cycle arrest. Accumulation of phosphorylated sphingoid long chain bases (LCBPs) stimulates calcium influx and activates calcineurin signaling. Involved in heat-stress resistance
Gene Name:
LCB5
Uniprot ID:
Q06147
Molecular weight:
77564.60156
Reactions
ATP + sphinganine → ADP + sphinganine 1-phosphate.
ATP + phytosphingosine → ADP + phytosphingosine 1-phosphate.
Protein Details
7. Dihydrosphingosine 1-phosphate phosphatase LCB3
General function:
Involved in catalytic activity
Specific function:
Dihydrosphingosine 1-phosphate phosphatase required for efficient ceramide synthesis from exogenous sphingoid bases. Involved in endocytosis and calcium-mediated signaling
Gene Name:
LCB3
Uniprot ID:
P47013
Molecular weight:
47371.30078
Reactions
Protein Details
8. Dihydrosphingosine 1-phosphate phosphatase YSR3
General function:
Involved in catalytic activity
Specific function:
Dihydrosphingosine 1-phosphate phosphatase required for efficient ceramide synthesis from exogenous sphingoid bases. Involved in endocytosis and calcium-mediated signaling
Gene Name:
YSR3
Uniprot ID:
P23501
Molecular weight:
46487.69922
Reactions
Protein Details
9. Sphingolipid C4-hydroxylase SUR2
General function:
Involved in iron ion binding
Specific function:
Required for hydroxylation of C-4 in the sphingoid moiety of ceramide. Involved in the response to syringomycin
Gene Name:
SUR2
Uniprot ID:
P38992
Molecular weight:
40734.0
Reactions