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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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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 [Peters90]


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."

Peters90: 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
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 21, 2014, biocyc14.