Phytosphingosine 1-phosphate (YMDB00762)

Identification

YMDB ID

YMDB00762

Name

Phytosphingosine 1-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Phytosphingosine 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

MOL SDF PDB SMILES InChI

Synonyms

Phytosphingosine 1-phosphoric acid

CAS number

Not Available

Weight

Average: 397.4871
Monoisotopic: 397.259324529

InChI Key

AYGOSKULTISFCW-KSZLIROESA-N

InChI

InChI=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 Name

phytosphingosine 1-phosphate

Chemical Formula

C₁₈H₄₀NO₆P

SMILES

CCCCCCCCCCCCCC[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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Phosphosphingolipids

Direct Parent

Phosphosphingolipids

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 Framework

Aliphatic acyclic compounds

External Descriptors

sphingoid 1-phosphate (CHEBI:46970 )
Sphingoid base 1-phosphates (LMSP01050003 )

Physical Properties

State

Not Available

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	0.017 g/L	ALOGPS
logP	3.01	ALOGPS
logP	2.56	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	9.37	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	133.24 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	103.16 m³·mol⁻¹	ChemAxon
Polarizability	45.65 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

endoplasmic reticulum

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Not Available

SMPDB Reactions

Not 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 Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-3931000000-49e5f2c92381acd34655	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uea-0139000000-51052f2317a76cb4dc12	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000y-3953000000-99b4d8dc28f886ef18cf	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0005-7940000000-b68e69385ea0b2c2f275	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002b-9238000000-234612104800bd27157d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9210000000-41a7cf446a4c892aa84d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-1972c746e1aeacd464e8	JSpectraViewer

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:

Resource	Link
CHEBI ID	46970
HMDB ID	Not Available
Pubchem Compound ID	10883829
Kegg ID	Not Available
ChemSpider ID	Not Available
FOODB ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not 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

Structure for #<Compound:0xac56c3ac>

Enzymes

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