Metabolic Modeling Tutorial
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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
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: nitrite

Synonyms: NO2, NO2-

Superclasses: an ion an anion

Chemical Formula: NO2

Molecular Weight: 46.005 Daltons

Monoisotopic Molecular Weight: 47.0007282815 Daltons

SMILES: N([O-])=O

InChI: InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1

InChIKey: InChIKey=IOVCWXUNBOPUCH-UHFFFAOYSA-M

Unification Links: CAS:7697-37-2 , CAS:14797-65-0 , ChEBI:16301 , ChemSpider:921 , HMDB:HMDB02786 , IAF1260:33805 , KEGG:C00088 , MetaboLights:MTBLC16301 , PubChem:946

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -65.91206 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

alkylnitronates degradation , nitrate reduction V (assimilatory) :
ammonium + 3 NAD(P)+ + 2 H2O ← nitrite + 3 NAD(P)H + 5 H+

ammonia oxidation II (anaerobic) , intra-aerobic nitrite reduction , nitrate reduction VII (denitrification) , nitrifier denitrification :
nitric oxide + an oxidized c-type cytochrome + H2O ← nitrite + a reduced c-type cytochrome + 2 H+

nitrate reduction II (assimilatory) , nitrate reduction VI (assimilatory) :
ammonium + 6 an oxidized ferredoxin + 2 H2O ← nitrite + 6 a reduced ferredoxin + 8 H+

nitrate reduction IV (dissimilatory) :
ammonia + 6 an oxidized c-type cytochrome + 2 H2O ← nitrite + 6 a reduced c-type cytochrome + 7 H+

nitrite oxidation :
2 a reduced c-type cytochrome[out] + nitrate[in] + 2 H+[in] ← 2 an oxidized c-type cytochrome[out] + nitrite[in] + H2O[in]

Not in pathways:
ammonia + 6 an oxidized cytochrome c552 + 2 H2O ← nitrite + 6 a reduced cytochrome c552 + 7 H+
ammonium + 3 NAD+ + 2 H2O ← nitrite + 3 NADH + 5 H+

Reactions known to produce the compound:

2,4-dinitrotoluene degradation :
2,4-dinitrotoluene + NADH + oxygen → 4-methyl-5-nitrocatechol + nitrite + NAD+
4-methyl-5-nitrocatechol + NADPH + oxygen → 2-hydroxy-5-methylquinone + nitrite + NADP+ + H+ + H2O

2,6-dinitrotoluene degradation :
2,6-dinitrotoluene + NADH + oxygen → 3-methyl-4-nitrocatechol + nitrite + NAD+

2-nitrophenol degradation :
2-nitrophenol + NADPH + oxygen + 3 H+ → catechol + nitrite + NADP+ + H2O

2-nitrotoluene degradation :
2-nitrotoluene + H+ + oxygen → 3-methylcatechol + nitrite

4-nitrophenol degradation I :
4-nitrophenol + NAD(P)H + oxygen + H+ → 1,4-benzoquinone + nitrite + NAD(P)+ + H2O

4-nitrophenol degradation II :
4-nitrocatechol + NAD(P)H + oxygen → 2-hydroxy-1,4-benzoquinone + nitrite + NAD(P)+ + H2O + H+

5-nitroanthranilate degradation :
4-nitro-6-oxohepta-2,4-dienedioate → 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + nitrite

alkylnitronates degradation :
ethylnitronate + oxygen → acetaldehyde + nitrite + [unspecified degradation products]

ammonia oxidation I (aerobic) , ammonia oxidation IV (autotrophic ammonia oxidizers) :
4 an oxidized c-type cytochrome[out] + hydroxylamine[in] + H2O[in] → 4 a reduced c-type cytochrome[out] + nitrite[in] + 5 H+[in]

ammonia oxidation III :
pyruvic oxime + oxygen → pyruvate + nitrite + H+

nitrate reduction II (assimilatory) :
nitrite + NAD+ + H2O ← nitrate + NADH + H+

nitrate reduction III (dissimilatory) , nitrate reduction VIII (dissimilatory) :
nitrate + a menaquinol[inner membrane] + 2 H+nitrite + a menaquinone[inner membrane] + H2O + 2 H+[periplasmic space]

nitrate reduction IV (dissimilatory) :
2 a reduced c-type cytochrome[out] + nitrate[in] + 2 H+[in] → 2 an oxidized c-type cytochrome[out] + nitrite[in] + H2O[in]

nitrate reduction V (assimilatory) :
nitrite + NADP+ + H2O ← nitrate + NADPH + H+

nitrate reduction VI (assimilatory) :
nitrite + 2 an oxidized ferredoxin + H2O ← nitrate + 2 a reduced ferredoxin

nitrobenzene degradation II :
nitrobenzene + H+ + oxygen → catechol + nitrite

nitroethane degradation :
nitroethane + oxygen + H2O → acetaldehyde + nitrite + hydrogen peroxide + H+

nitroglycerin degradation :
nitroglycerin + NAD(P)H → nitrite + 1,2-dinitroglycerol + NAD(P)+
nitroglycerin + NAD(P)H → 1,3-dinitroglycerol + nitrite + NAD(P)+
1,3-dinitroglycerol + NAD(P)H → 1-mononitroglycerol + nitrite + NAD(P)+
1,2-dinitroglycerol + NAD(P)H → 1-mononitroglycerol + nitrite + NAD(P)+
1,2-dinitroglycerol + NAD(P)H → 2-mononitroglycerol + nitrite + NAD(P)+

Not in pathways:
3-aci-nitropropanoate + oxygen + H2O → malonate semialdehyde + nitrite + hydrogen peroxide
nitrate[periplasmic space] + an ubiquinol[inner membrane]nitrite[periplasmic space] + an ubiquinone[inner membrane] + H2O[periplasmic space]
a nitroalkane + oxygen + H2O → an aldehyde or ketone + nitrite + hydrogen peroxide + H+
2-nitroimidazole + H2O → 1,3-dihydro-2H-imidazol-2-one + nitrite + H+
5-nitrosalicylate + oxygen → 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + nitrite + H+
hydroxylamine + 4 an oxidized c-type cytochrome + oxygen → nitrite + 4 a reduced c-type cytochrome + H2O + H+

Reactions known to both consume and produce the compound:

ammonia oxidation II (anaerobic) :
nitrite + a reduced electron acceptor + 3 H+ ↔ hydroxylamine + an oxidized electron acceptor + H2O

nitrate reduction I (denitrification) :
nitrate[in] + an electron-transfer-related quinol ↔ nitrite[in] + an electron-transfer-related quinone + H2O[in]
nitric oxide + an oxidized cytochrome c551 + H2O ↔ nitrite + a reduced cytochrome c551 + 2 H+

nitrate reduction VII (denitrification) :
nitrate[in] + an electron-transfer-related quinol ↔ nitrite[in] + an electron-transfer-related quinone + H2O[in]

In Reactions of unknown directionality:

Not in pathways:
3-nitrotoluene + NADH + oxygen = 4-methylcatechol + nitrite + NAD+
1-mononitroglycerol + NAD(P)H = glycerol + nitrite + NAD(P)+
2-mononitroglycerol + NAD(P)H = glycerol + nitrite + NAD(P)+
3 nitrite + 2 H+ = 2 nitric oxide + nitrate + H2O
nitrite + an oxidized electron acceptor + H2O = nitrate + a reduced electron acceptor
nitrite + NAD(P)+ + H2O = nitrate + NAD(P)H + H+

In Transport reactions:
nitrite[periplasmic space]nitrite[cytosol] ,
nitrate[periplasmic space] + nitrite[cytosol] → nitrate[cytosol] + nitrite[periplasmic space] ,
nitrite[cytosol] + H+[periplasmic space]nitrite[periplasmic space] + H+[cytosol]

In Redox half-reactions:
nitrate[out] + 2 H+[out] + 2 e-nitrite[out] + H2O[out] ,
nitrate[in] + 2 H+[in] + 2 e-nitrite[in] + H2O[in] ,
nitrate + 2 H+ + 2 e-nitrite + H2O ,
nitrite[in] + 5 H+[in] + 4 e- → hydroxylamine[in] + H2O[in] ,
nitrite + 2 H+ + e- → nitric oxide + H2O ,
nitrite + 8 H+ + 6 e- → ammonium + 2 H2O

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

Inhibitor (Competitive) of: cyanase [Little87, Comment 1] , ethylnitronate monooxygenase [Francis09]

Inhibitor (Mechanism unknown) of: formate dehydrogenase [Axley90] , nitrogenase [Meyer81] , NAD-dependent formate dehydrogenase [Jollie91]


References

Axley90: Axley MJ, Grahame DA, Stadtman TC (1990). "Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component." J Biol Chem 1990;265(30);18213-8. PMID: 2211698

Francis09: Francis K, Gadda G (2009). "Kinetic evidence for an anion binding pocket in the active site of nitronate monooxygenase." Bioorg Chem 37(5);167-72. PMID: 19683782

Jollie91: Jollie DR, Lipscomb JD (1991). "Formate dehydrogenase from Methylosinus trichosporium OB3b. Purification and spectroscopic characterization of the cofactors." J Biol Chem 266(32);21853-63. PMID: 1657982

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

Little87: Little RM, Anderson PM (1987). "Structural properties of cyanase. Denaturation, renaturation, and role of sulfhydryls and oligomeric structure in catalytic activity." J Biol Chem 1987;262(21);10120-6. PMID: 3301828

Meyer81: Meyer J (1981). "Comparison of carbon monoxide, nitric oxide, and nitrite as inhibitors of the nitrogenase from Clostridium pasteurianum." Arch Biochem Biophys 1981;210(1);246-56. PMID: 6945823


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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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