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Phytosphingosine 1-phosphate (YMDB00762)

Identification
YMDB IDYMDB00762
NamePhytosphingosine 1-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPhytosphingosine 1-phosphate 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
  • Phytosphingosine 1-phosphoric acid
CAS numberNot Available
WeightAverage: 397.4871
Monoisotopic: 397.259324529
InChI KeyAYGOSKULTISFCW-KSZLIROESA-N
InChIInChI=1S/C18H40NO6P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(20)18(21)16(19)15-25-26(22,23)24/h16-18,20-21H,2-15,19H2,1H3,(H2,22,23,24)/t16-,17+,18-/m0/s1
IUPAC Name{[(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl]oxy}phosphonic acid
Traditional IUPAC Namephytosphingosine 1-phosphate
Chemical FormulaC18H40NO6P
SMILESCCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@@H](N)COP(O)(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassPhosphosphingolipids
Direct ParentPhosphosphingolipids
Alternative Parents
Substituents
  • Sphingoid-1-phosphate or derivatives
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • 1,3-aminoalcohol
  • 1,2-diol
  • 1,2-aminoalcohol
  • Secondary alcohol
  • Organopnictogen compound
  • Organic nitrogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Amine
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.017 g/LALOGPS
logP3.01ALOGPS
logP2.56ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)1.51ChemAxon
pKa (Strongest Basic)9.37ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area133.24 ŲChemAxon
Rotatable Bond Count18ChemAxon
Refractivity103.16 m³·mol⁻¹ChemAxon
Polarizability45.65 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 PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG Reactions
Phytosphingosine 1-phosphate → 2-hydroxyhexadecanal + O-Phosphoethanolamine
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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-3931000000-49e5f2c92381acd34655JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uea-0139000000-51052f2317a76cb4dc12JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000y-3953000000-99b4d8dc28f886ef18cfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-7940000000-b68e69385ea0b2c2f275JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-9238000000-234612104800bd27157dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9210000000-41a7cf446a4c892aa84dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-1972c746e1aeacd464e8JSpectraViewer
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
  • Cowart, L. A., Shotwell, M., Worley, M. L., Richards, A. J., Montefusco, D. J., Hannun, Y. A., Lu, X. (2010). "Revealing a signaling role of phytosphingosine-1-phosphate in yeast." Mol Syst Biol 6:349.20160710
  • 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
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID46970
HMDB IDNot Available
Pubchem Compound ID10883829
Kegg IDNot Available
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. 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
2. 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
3. Sphingosine-1-phosphate lyase
General function:
Involved in carboxy-lyase activity
Specific function:
Cleaves phosphorylated sphingoid bases (PSBs), such as sphingosine-1-phosphate, into fatty aldehydes and phosphoethanolamine
Gene Name:
DPL1
Uniprot ID:
Q05567
Molecular weight:
65565.10156
Reactions
Sphinganine 1-phosphate → phosphoethanolamine + palmitaldehyde.
Protein Details
4. 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
5. 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