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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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MetaCyc Compound: formaldehyde

Synonyms: formalin, methanal, formol

Superclasses: an aldehyde or ketone an aldehyde an n-alkanal

Chemical Formula: CH2O

Molecular Weight: 30.026 Daltons

Monoisotopic Molecular Weight: 30.0105646863 Daltons

SMILES: [CH2]=O

InChI: InChI=1S/CH2O/c1-2/h1H2

InChIKey: InChIKey=WSFSSNUMVMOOMR-UHFFFAOYSA-N

Unification Links: CAS:50-00-0 , ChEBI:16842 , ChemSpider:692 , DrugBank:DB03843 , HMDB:HMDB01426 , IAF1260:33726 , KEGG:C00067 , MetaboLights:MTBLC16842 , PubChem:712

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -10.65776 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

4-hydroxycoumarin and dicoumarol biosynthesis :
2 4-hydroxycoumarin + formaldehyde → dicoumarol + H2O

formaldehyde assimilation I (serine pathway) :
formaldehyde + a tetrahydrofolate → a 5,10-methylene-tetrahydrofolate + H2O

formaldehyde assimilation II (RuMP Cycle) , formaldehyde oxidation I :
hexulose 6-phosphate ← D-ribulose 5-phosphate + formaldehyde

formaldehyde assimilation III (dihydroxyacetone cycle) :
formaldehyde + D-xylulose 5-phosphate → dihydroxyacetone + D-glyceraldehyde 3-phosphate

formaldehyde oxidation III (mycothiol-dependent) :
formaldehyde + mycothiol → S-hydroxymethylmycothiol

formaldehyde oxidation IV (thiol-independent) :
formaldehyde + NAD+ + H2O → formate + NADH + 2 H+

formaldehyde oxidation V (H4MPT pathway) :
5,10-methylene-tetrahydromethanopterin + H2O ← formaldehyde + tetrahydromethanopterin

furaneol biosynthesis :
norfuraneol + formaldehyde → 4-hydroxy-5-methyl-2-methylene-3(2H)-furanone + H2O

NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) :
an aldehyde + NAD+ + H2O → a carboxylate + NADH + 2 H+
an aldehyde + NADP+ + H2O → a carboxylate + NADPH + 2 H+

Not in pathways:
an aldehyde + FMNH2 + oxygen → hν + a carboxylate + FMN + H2O + 2 H+
an aldehyde + oxygen + H2O → a carboxylate + hydrogen peroxide + H+

Reactions known to produce the compound:

5,5'-dehydrodivanillate degradation :
5,5'-dehydrodivanillate + NADH + oxygen + H+ → 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl + formaldehyde + NAD+ + H2O

caffeine degradation III (bacteria, via demethylation) :
7-methylxanthine + NAD(P)H + oxygen + H+ → xanthine + formaldehyde + NAD(P)+ + H2O
caffeine + NAD(P)H + oxygen + H+ → theobromine + formaldehyde + NAD(P)+ + H2O
paraxanthine + NAD(P)H + oxygen + H+ → 7-methylxanthine + formaldehyde + NAD(P)+ + H2O
theobromine + NAD(P)H + oxygen + H+ → 7-methylxanthine + formaldehyde + NAD(P)+ + H2O
caffeine + NAD(P)H + oxygen + H+ → paraxanthine + formaldehyde + NAD(P)+ + H2O

colchicine biosynthesis :
demecolcine + NADPH + oxygen + H+ → deacetylcolchicine + formaldehyde + NADP+ + H2O

creatinine degradation I :
sarcosine + oxygen + H2O → glycine + formaldehyde + hydrogen peroxide
sarcosine + an oxidized electron-transfer flavoprotein + H2O + H+ → glycine + formaldehyde + a reduced electron-transfer flavoprotein

creatinine degradation II :
sarcosine + oxygen + H2O → glycine + formaldehyde + hydrogen peroxide
sarcosine + an oxidized electron-transfer flavoprotein + H2O + H+ → glycine + formaldehyde + a reduced electron-transfer flavoprotein

dimethyl sulfide degradation I :
methanethiol + oxygen + H2O → formaldehyde + hydrogen sulfide + hydrogen peroxide
dimethyl sulfide + NADH + oxygen + H+ → methanethiol + formaldehyde + NAD+ + H2O

dimethyl sulfide degradation II (oxidation) :
methanesulfonate + NADH + oxygen → formaldehyde + sulfite + NAD+ + H2O
dimethyl sulfone + 2 FMNH2 + 2 oxygen → methanesulfonate + formaldehyde + 2 FMN + 2 H2O + 3 H+

glycine betaine degradation I :
sarcosine + oxygen + H2O → glycine + formaldehyde + hydrogen peroxide
dimethylglycine + an oxidized electron-transfer flavoprotein + H2O + H+ → sarcosine + formaldehyde + a reduced electron-transfer flavoprotein

melatonin degradation I :
melatonin + a reduced flavoprotein + oxygen → N-acetyl-serotonin + an oxidized flavoprotein + formaldehyde + H2O

methanesulfonate degradation :
methanesulfonate + NADH + oxygen → formaldehyde + sulfite + NAD+ + H2O

methanol oxidation to formaldehyde I :
methanol + 2 an oxidized cytochrome cLformaldehyde + 2 a reduced cytochrome cL + 2 H+

methanol oxidation to formaldehyde III :
methanol + an oxidized electron acceptor → formaldehyde + a reduced electron acceptor

methanol oxidation to formaldehyde IV :
methanol + oxygen → hydrogen peroxide + formaldehyde

methylamine degradation I :
methylamine + an oxidized amicyanin + H2O → formaldehyde + ammonium + a reduced amicyanin

methylamine degradation II :
N-methyl-L-glutamate + an oxidized electron acceptor + H2O → L-glutamate + formaldehyde + a reduced electron acceptor

morphine biosynthesis :
oripavine + 2-oxoglutarate + oxygen → morphinone + formaldehyde + succinate + CO2
thebaine + 2-oxoglutarate + oxygen → oripavine + formaldehyde + succinate + CO2
thebaine + 2-oxoglutarate + oxygen → neopinone + formaldehyde + succinate + CO2
codeine + 2-oxoglutarate + oxygen → morphine + formaldehyde + succinate + CO2

nevadensin biosynthesis :
gardenin B + 2-oxoglutarate + oxygen → nevadensin + formaldehyde + succinate + CO2
8-hydroxy-salvigenin + 2-oxoglutarate + oxygen → pilosin + formaldehyde + succinate + CO2

nicotine degradation I :
4-methylaminobutanoate + oxygen + H2O → 4-aminobutanoate + formaldehyde + hydrogen peroxide

nicotine degradation IV :
(S)-nicotine + H2O → nornicotine + formaldehyde + 2 H+

theophylline degradation :
theophylline + NAD(P)H + oxygen + H+ → 3-methylxanthine + formaldehyde + NAD(P)+ + H2O
1-methylxanthine + NAD(P)H + oxygen + H+ → xanthine + formaldehyde + NAD(P)+ + H2O
3-methylxanthine + NAD(P)H + oxygen + H+ → xanthine + formaldehyde + NAD(P)+ + H2O
theophylline + NAD(P)H + oxygen + H+ → 1-methylxanthine + formaldehyde + NAD(P)+ + H2O

trimethylamine degradation :
trimethylamine N-oxide + H+ → dimethylamine + formaldehyde
dimethylamine + NADPH + oxygen + H+ → methylamine + formaldehyde + NADP+ + H2O

vanillin and vanillate degradation II :
vanillate + NADH + oxygen + H+ → protocatechuate + formaldehyde + NAD+ + H2O

Not in pathways:
dimethylglycine + oxygen + H2O → hydrogen peroxide + formaldehyde + sarcosine
N6-methyl-L-lysine + oxygen + H2O → hydrogen peroxide + formaldehyde + L-lysine
N-methyl-L-tryptophan + oxygen + H2O → hydrogen peroxide + formaldehyde + L-tryptophan
4-methoxybenzoate + a reduced electron acceptor + oxygen → 4-hydroxybenzoate + formaldehyde + an oxidized electron acceptor + H2O
a methylated nucleobase within DNA + 2-oxoglutarate + oxygen → a nucleobase within DNA + CO2 + formaldehyde + succinate + H+
N3-methylcytosine + 2-oxoglutarate + oxygen → cytosine + CO2 + formaldehyde + succinate + H+
a [protein] N6,N6-dimethyl-L-lysine + 2 2-oxoglutarate + 2 oxygen + H+ → a [protein]-L-lysine + 2 succinate + 2 formaldehyde + 2 CO2
a [protein] N6-methyl-L-lysine + 2-oxoglutarate + oxygen + H+ → a [protein]-L-lysine + succinate + formaldehyde + CO2
dimethyl sulfone + FMNH2 + oxygen → methylsulfonyl + formaldehyde + FMN + H2O + 2 H+
N1-methyladenine + 2-oxoglutarate + oxygen → adenine + CO2 + formaldehyde + succinate
a N-methyl L-amino acid + oxygen + H2O → an L-amino acid + formaldehyde + hydrogen peroxide

8-amino-7-oxononanoate biosynthesis II :
a long-chain acyl-[acp] + 2 a reduced flavodoxin + 3 oxygen → a pimeloyl-[acp] + an n-alkanal + 2 an oxidized flavodoxin + 3 H2O + H+

ceramide degradation :
a sphingoid 1-phosphate → phosphoryl-ethanolamine + an aldehyde

two-component alkanesulfonate monooxygenase :
an alkanesulfonate + FMNH2 + oxygen → an aldehyde + sulfite + FMN + H2O + 2 H+


a primary amine[periplasmic space] + H2O[periplasmic space] + oxygen[periplasmic space]an aldehyde[periplasmic space] + ammonium[periplasmic space] + hydrogen peroxide[periplasmic space]
an aliphatic amine + H2O + oxygen → an aldehyde + ammonium + hydrogen peroxide
a monoamine + H2O + oxygen → an aldehyde + a primary amine + hydrogen peroxide
a primary alcohol + oxygen → hydrogen peroxide + an aldehyde


a nitroalkane + oxygen + H2O → an aldehyde or ketone + nitrite + hydrogen peroxide + H+

Reactions known to both consume and produce the compound:

formaldehyde oxidation II (glutathione-dependent) :
S-hydroxymethylglutathione → formaldehyde + glutathione

Not in pathways:
a primary alcohol + NAD+an aldehyde + NADH + H+

In Reactions of unknown directionality:

methanol oxidation to formaldehyde II :
methanol + NAD+ = formaldehyde + NADH + H+

Not in pathways:
erythrulose 1-phosphate = formaldehyde + dihydroxyacetone phosphate
bromochloromethane + H2O = bromide + chloride + formaldehyde + 2 H+
N,N-dimethylaniline-N-oxide = formaldehyde + N-methylaniline
acetol + NADPH + oxygen = acetate + formaldehyde + NADP+ + H2O
dichloromethane + H2O = formaldehyde + 2 chloride + 2 H+
trimethylamine + an oxidized electron-transfer flavoprotein + H2O = dimethylamine + formaldehyde + a reduced electron-transfer flavoprotein
dimethylamine + an oxidized electron-transfer flavoprotein + H2O = formaldehyde + methylamine + a reduced electron-transfer flavoprotein
a [protein] N6,N6-dimethyl-L-lysine + 2-oxoglutarate + oxygen = a [protein] N6-methyl-L-lysine + succinate + formaldehyde + CO2
methanol + hydrogen peroxide = formaldehyde + 2 H2O
2-dehydropantoate = formaldehyde + 3-methyl-2-oxobutanoate
2 formaldehyde + H2O = methanol + formate + H+
pyruvate + formaldehyde + H+ = acetol + CO2


an n-alkanal + NAD(P)+ = an alk-2-enal + NAD(P)H + H+
an n-alkanal + NADP+ = an alk-2-enal + NADPH + H+
a 7,8-dihydroxy-long-chain acyl-[acp] + a reduced flavodoxin + oxygen = 7-oxoheptanoyl-[acyl-carrier-protein] + an n-alkanal + an oxidized flavodoxin + 2 H2O


an aldehyde + NAD(P)+ + H2O = a carboxylate + NAD(P)H + 2 H+
an aldehyde + 2 an oxidized ferredoxin + H2O = a carboxylate + 2 a reduced ferredoxin + 3 H+
an aldehyde + an oxidized electron acceptor + H2O = a carboxylate + a reduced electron acceptor + H+
an aldehyde + pyrroloquinoline quinone + H2O = a carboxylate + pyrroloquinoline quinol + H+
an aldehyde[periplasmic space] + FAD[periplasmic space] + H2O[periplasmic space] = a carboxylate[periplasmic space] + FADH2[periplasmic space]
an aliphatic amine + an oxidized cytochrome c550 + H2O = an aldehyde + ammonium + a reduced cytochrome c550
an alkylamine + 2 an oxidized cytochrome c550 + H2O = an aldehyde + ammonium + 2 a reduced cytochrome c550
a 2-oxo carboxylate + H+ = an aldehyde + CO2
an alcohol + NADP+ = an aldehyde + NADPH + H+
a primary alcohol + an oxidized electron acceptor = an aldehyde + a reduced electron acceptor
a primary alcohol + 2 an oxidized cytochrome cL = an aldehyde + 2 a reduced cytochrome cL
an alcohol + NAD(P)+ = an aldehyde + NAD(P)H + H+
a primary alcohol + an oxidized azurin = an aldehyde + a reduced azurin
a 1-O-(alk-1-enyl)glycero-3-phosphocholine + H2O = sn-glycero-3-phosphocholine + an aldehyde
a 1-alkenylglycerophosphoethanolamine + H2O = sn-glycero-3-phosphoethanolamine + an aldehyde
a primary alcohol + 2 an oxidized cytochrome c550 = an aldehyde + 2 a reduced cytochrome c550

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

Inhibitor (Mechanism unknown) of: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Powers76, Comment 1] , methylglutamate dehydrogenase [Bamforth77] , 2-protocatechuoylphloroglucinolcarboxylate esterase [Child63] , rutinase [HAY61] , aspartate-semialdehyde dehydrogenase [Peters90a]


References

Bamforth77: Bamforth CW, Large PJ (1977). "Solubilization, partial purification and properties of N-methylglutamate dehydrogenase from Pseudomonas aminovorans." Biochem J 161(2);357-70. PMID: 15545

Child63: Child JJ, Simpson FJ, Westlake DWS (1963). "Degradation of rutin by Aspergillus flavus. Production, purification and characterization of an esterase." Can J Microbiol 9:653-664.

HAY61: HAY GW, WESTLAKE DW, SIMPSON FJ (1961). "Degradation of rutin by Aspergillus flavus. Purification and characterization of rutinase." Can J Microbiol 7;921-32. PMID: 13905544

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

Peters90a: Peters, P, Galinski, EA, Truper, HG "The biosynthesis of ectoine." FEMS Microbiology Letters 71:157-162 (1990).

Powers76: Powers SG, Snell EE (1976). "Ketopantoate hydroxymethyltransferase. II. Physical, catalytic, and regulatory properties." J Biol Chem 1976;251(12);3786-93. PMID: 6463


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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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