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MetaCyc Compound: spermidine

Synonyms: N-(3-aminopropyl)butane-1,4-diamine

Superclasses: an amine an aliphatic amine an aliphatic diamine an aliphatic alpha,omega-diamine

Chemical Formula: C7H22N3

Molecular Weight: 148.27 Daltons

Monoisotopic Molecular Weight: 145.1578976255 Daltons

spermidine compound structure

SMILES: C([N+])CC[N+]CCCC[N+]

InChI: InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2/p+3

InChIKey: InChIKey=ATHGHQPFGPMSJY-UHFFFAOYSA-Q

Unification Links: CAS:124-20-9 , ChEBI:57834 , ChemSpider:5360248 , HMDB:HMDB01257 , IAF1260:34593 , KEGG:C00315 , MetaboLights:MTBLC57834 , PubChem:6992097

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): 227.9461 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

glutathionylspermidine biosynthesis :
spermidine + glutathione + ATP → glutathionylspermidine + ADP + phosphate + H+

homospermidine biosynthesis :
putrescine + spermidine → propane-1,3-diamine + sym-homospermidine

hypusine biosynthesis :
spermidine + NAD+ → dehydrospermidine + NADH + H+

petrobactin biosynthesis :
spermidine + citrate + ATP → N-citryl-spermidine + AMP + diphosphate + H+
N-citryl-spermidine + spermidine + ATP → N8,N'8-citryl-bis(spermidine) + AMP + diphosphate + H+
N1-(3,4-dihydroxybenzoyl)-N8-citryl-spermidine + spermidine + ATP → N1-(3,4-dihydroxybenzoyl)-N8,N'8-citryl-bis(spermidine) + AMP + diphosphate + H+

spermidine hydroxycinnamic acid conjugates biosynthesis :
3 feruloyl-CoA + spermidine → triferuloyl spermidine + 3 coenzyme A + 3 H+
3 4-coumaryl-CoA + spermidine → tricoumaroyl spermidine + 3 coenzyme A + 3 H+
3 caffeoyl-CoA + spermidine → tricaffeoyl spermidine + 3 coenzyme A + 3 H+

spermine and spermidine degradation I :
acetyl-CoA + spermidineN1-acetylspermidine + coenzyme A + H+

spermine and spermidine degradation II :
spermidine + oxygen + H2O → propane-1,3-diamine + 4-aminobutanal + hydrogen peroxide

spermine and spermidine degradation III :
spermidine + oxygen + H2O → putrescine + 3-aminopropanal + hydrogen peroxide

spermine biosynthesis , superpathway of polyamine biosynthesis II :
spermidine + S-adenosyl 3-(methylthio)propylamine → spermine + S-methyl-5'-thioadenosine + H+

Not in pathways:
an aliphatic amine + H2O + oxygen → an aldehyde + ammonium + hydrogen peroxide

Not in pathways:
an amine + S-adenosyl-L-methionine → S-adenosyl-L-homocysteine + a methylated amine

Reactions known to produce the compound:

β-alanine biosynthesis IV , spermine and spermidine degradation III :
spermine + oxygen + H2O → spermidine + 3-aminopropanal + hydrogen peroxide

spermidine biosynthesis II :
carboxyspermidine + H+spermidine + CO2

spermidine biosynthesis III :
N1-(3-aminopropyl)agmatine + H2O → spermidine + urea

spermine and spermidine degradation I :
N1-acetylspermine + oxygen + H2O → spermidine + 3-acetamidopropanal + hydrogen peroxide
spermine + oxygen + H2O → spermidine + 3-aminopropanal + hydrogen peroxide

Not in pathways:
N1-acetylspermine + oxygen + H2O → spermidine + 3-acetamidopropanal + hydrogen peroxide

Reactions known to both consume and produce the compound:

spermidine biosynthesis I :
putrescine + S-adenosyl 3-(methylthio)propylamine ↔ spermidine + S-methyl-5'-thioadenosine + H+

Not in pathways:
glutathionylspermidine + H2O ↔ glutathione + spermidine

Not in pathways:
an aliphatic α,ω-diamine + 2-oxoglutarate ↔ L-glutamate + an aliphatic ω-aminoaldehyde

In Reactions of unknown directionality:

Not in pathways:
N8-acetylspermidine + H2O = spermidine + acetate
2 4-coumaryl-CoA + spermidine = N1,N8-bis(coumaroyl)-spermidine + 2 coenzyme A + 2 H+
2 sinapoyl-CoA + spermidine = N1,N8-bis(sinapoyl)-spermidine + 2 coenzyme A + 2 H+
2 S-adenosyl 3-(methylthio)propylamine + spermidine = 2 S-methyl-5'-thioadenosine + N4-bis(aminopropyl)spermidine + 2 H+
S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + N4-aminopropylspermidine + H+
S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+
spermidine + an [eIF5A-precursor]-lysine = an [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine + H+
spermidine + an oxidized unknown electron acceptor + H2O = propane-1,3-diamine + 4-aminobutanal + an reduced unknown electron acceptor

Not in pathways:
acetyl-CoA + an aliphatic α,ω-diamine = an aliphatic N-acetyl-diamine + coenzyme A + H+

Not in pathways:
an aliphatic amine + an oxidized cytochrome c550 + H2O = an aldehyde + ammonium + a reduced cytochrome c550

Not in pathways:
3'-phosphoadenylyl-sulfate + an amine = adenosine 3',5'-bisphosphate + a sulfamate

In Transport reactions:
spermidine[cytosol] + H+[periplasmic space]spermidine[periplasmic space] + H+[cytosol] ,
ATP + spermidine[periplasmic space] + H2O → ADP + spermidine[cytosol] + phosphate + H+

Enzymes activated by spermidine, sorted by the type of activation, are:

Activator (Mechanism unknown) of: acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase [Vallari82]

Enzymes inhibited by spermidine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: arginine decarboxylase, degradative [Blethen68] , ornithine decarboxylase [Applebaum77] , L-lysine monooxygenase [Nakazawa72]

Inhibitor (Mechanism unknown) of: arginine decarboxylase, biosynthetic [Wu73, Comment 1] , lysine decarboxylase [Wertheimer83] , spermidine synthase [Bowman73, Comment 2] , adenosylmethionine decarboxylase [Tabor85, Kashiwagi88] , dihydrofolate reductase [Baccanari75] , ornithine succinyltransferase [Tricot94]

This compound has been characterized as an alternative substrate of the following enzymes: polyamine aminotransferase , spermidine synthase , putrescine oxidase , diamine transaminase , histamine oxidase , putrescine aminotransferase , agmatine aminopropyltransferase


References

Applebaum77: Applebaum DM, Dunlap JC, Morris DR (1977). "Comparison of the biosynthetic and biodegradative ornithine decarboxylases of Escherichia coli." Biochemistry 1977;16(8);1580-4. PMID: 15587

Baccanari75: Baccanari D, Phillips A, Smith S, Sinski D, Burchall J (1975). "Purification and properties of Escherichia coli dihydrofolate reductase." Biochemistry 1975;14(24);5267-73. PMID: 46

Blethen68: Blethen SL, Boeker EA, Snell EE (1968). "Argenine decarboxylase from Escherichia coli. I. Purification and specificity for substrates and coenzyme." J Biol Chem 1968;243(8);1671-7. PMID: 4870599

Bowman73: Bowman WH, Tabor CW, Tabor H (1973). "Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli." J Biol Chem 1973;248(7);2480-6. PMID: 4572733

Kashiwagi88: Kashiwagi K, Igarashi K (1988). "Adjustment of polyamine contents in Escherichia coli." J Bacteriol 170(7);3131-5. PMID: 3290196

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Nakazawa72: Nakazawa T, Hori K, Hayaishi O (1972). "Studies on monooxygenases. V. Manifestation of amino acid oxidase activity by L-lysine monooxygenase." J Biol Chem 247(11);3439-44. PMID: 4624115

Tabor83: Tabor CW, Tabor H (1983). "Putrescine aminopropyltransferase (Escherichia coli)." Methods Enzymol 1983;94;265-70. PMID: 6312268

Tabor85: Tabor CW, Tabor H (1985). "Polyamines in microorganisms." Microbiol Rev 1985;49(1);81-99. PMID: 3157043

Tricot94: Tricot C, Vander Wauven C, Wattiez R, Falmagne P, Stalon V (1994). "Purification and properties of a succinyltransferase from Pseudomonas aeruginosa specific for both arginine and ornithine." Eur J Biochem 224(3);853-61. PMID: 7523119

Vallari82: Vallari DS, Rock CO (1982). "Role of spermidine in the activity of sn-glycerol-3-phosphate acyltransferase from Escherichia coli." Arch Biochem Biophys 1982;218(2);402-8. PMID: 6760815

Wertheimer83: Wertheimer SJ, Leifer Z (1983). "Putrescine and spermidine sensitivity of lysine decarboxylase in Escherichia coli: evidence for a constitutive enzyme and its mode of regulation." Biochem Biophys Res Commun 114(2);882-8. PMID: 6349639

Wu73: Wu WH, Morris DR (1973). "Biosynthetic arginine decarboxylase from Escherichia coli. Purification and properties." J Biol Chem 1973;248(5);1687-95. PMID: 4571773


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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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