MetaCyc Compound Class: a sphingoid base

Synonyms: a sphingolipid long chain base, LCB

Superclasses: an alcoholan amino alcohol

Sphingoids (sphingoid bases, or long chain bases) are building blocks of sphingolipids. They are amino alcohols, composed predominantly of 18 carbon atoms. They are characterized by the presence of a hydroxyl group at C1 (and often also at C3), and an amine group at C2. The commonly known sphingoids include sphingosine, D-erythro-sphinganine (dihydrosphingosine), and phytosphingosine (4-hydroxysphinganine).

a sphingoid base compound structure

Child Classes: a 4-hydroxy-8-sphingenine (2), a sphinganine (3), a sphingoid 1-phosphate (3)

3-dehydrosphinganine (C20),
sphinganine (C20),

Citations: [Pata10]

SMILES: C(O)([R])C([N+])CO

Reactions known to consume the compound:

ceramide degradation :
a sphingoid base + ATP → a sphingoid 1-phosphate + ADP + H+

Reactions known to produce the compound:

ceramide degradation :
a ceramide + H2O → a sphingoid base + a fatty acid

β-D-glucuronide and D-glucuronate degradation :
a β-D-glucuronoside + H2O → D-glucopyranuronate + an alcohol

glycerophosphodiester degradation :
a glycerophosphodiester + H2O → an alcohol + sn-glycerol 3-phosphate + H+

phosphate acquisition :
a phosphate monoester + H2O → an alcohol + phosphate

Not in pathways:
an organic hydroperoxide + NADH + H+an alcohol + NAD+ + H2O
a 6-phospho-β-D-galactoside + H2O → D-galactopyranose 6-phosphate + an alcohol
an α-D-glucuronoside + H2O → D-glucopyranuronate + an alcohol
an α amino acid ester + H2O → an alcohol + an α amino acid + H+
a phosphate monoester + H2O → an alcohol + phosphate
RH + a reduced [NADPH-hemoprotein reductase] + oxygen → ROH + an oxidized [NADPH-hemoprotein reductase] + H2O
an oligosaccharide with β-L-arabinopyranose at the non-reducing end + H2O → β-L-arabinopyranose + an alcohol
an N-acetyl-β-D-hexosaminide + H2O → an N-acetyl-β-D-hexosamine + an alcohol
a carboxylic ester + H2O → an alcohol + a carboxylate + H+
an acetic ester + H2O → an alcohol + acetate + H+
a reduced thioredoxin + an organic hydroperoxide → an oxidized thioredoxin + an alcohol + H2O
a 6-O-(β-D-xylopyranosyl)-β-D-glucopyranoside + H2O → primeverose + an alcohol
an organic molecule + H2O + 2 oxygen → an alcohol + 2 superoxide + 2 H+
an N5-acyl-L-ornithine-ester + H2O → an N5-acyl-L-ornithine + an alcohol
α-L-fucoside + H2O → L-fucopyranose + an alcohol
a 2-deoxy-α-D-glucoside + H2O → 2-deoxy-D-glucose + an alcohol

In Reactions of unknown directionality:

Not in pathways:
an acyl-CoA + a sphingoid base = a ceramide + coenzyme A + H+

Not in pathways:
an alcohol + 3'-phosphoadenylyl-sulfate = adenosine 3',5'-bisphosphate + an organosulfate + H+
an alcohol + NAD(P)+ = an aldehyde + NAD(P)H + H+
an alcohol + NADP+ = an aldehyde + NADPH + H+
an alcohol + acetyl-CoA = an acetic ester + coenzyme A
trans-cinnamoyl-β-D-glucoside + an alcohol = alkyl cinnamate + D-glucopyranose
2 protein cysteines + an organic hydroperoxide = a protein disulfide + an alcohol + H2O
an organic molecule + an organic hydroperoxide = 2 an alcohol
an organic molecule + hydrogen peroxide = an alcohol + H2O

Enzymes activated by a sphingoid base, sorted by the type of activation, are:

Activator (Mechanism unknown) of: phosphoenolpyruvate carboxylase [Izui83]

Created 08-Apr-2010 by Zhang P, TAIR


Chao11: Chao DY, Gable K, Chen M, Baxter I, Dietrich CR, Cahoon EB, Guerinot ML, Lahner B, Lu S, Markham JE, Morrissey J, Han G, Gupta SD, Harmon JM, Jaworski JG, Dunn TM, Salt DE (2011). "Sphingolipids in the root play an important role in regulating the leaf ionome in Arabidopsis thaliana." Plant Cell 23(3);1061-81. PMID: 21421810

Izui83: Izui K, Matsuda Y, Kameshita I, Katsuki H, Woods AE (1983). "Phosphoenolpyruvate carboxylase of Escherichia coli. Inhibition by various analogs and homologs of phosphoenolpyruvate." J Biochem (Tokyo) 1983;94(6);1789-95. PMID: 6368527

Morales07: Morales PR, Dillehay DL, Moody SJ, Pallas DC, Pruett S, Allgood JC, Symolon H, Merrill AH (2007). "Safingol toxicology after oral administration to TRAMP mice: demonstration of safingol uptake and metabolism by N-acylation and N-methylation." Drug Chem Toxicol 30(3);197-216. PMID: 17613006

Pata10: Pata MO, Hannun YA, Ng CK (2010). "Plant sphingolipids: decoding the enigma of the Sphinx." New Phytol 185(3);611-30. PMID: 20028469

Thudichum84: Thudichum, J. L. W. (1884). "A Treatise on the Chemical Constitution of Brain." Bailliere, Tindall, and Cox, London.

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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