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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: nitrate

Synonyms: NO3, NO3-

Superclasses: an ion an anion

Component of:
silver nitrate
calcium nitrate tetrahydrate
sodium nitrate

Summary:
Nitrate is the conjugate base of nitric acid. It is a common electron acceptor for anaerobic bacteria (see nitrate reduction pathways), and is also the ultimate product of an ammonia oxidation process known as nitrification.

Chemical Formula: NO3

Molecular Weight: 62.005 Daltons

Monoisotopic Molecular Weight: 62.9956429036 Daltons

SMILES: N(=O)(=O)[O-]

InChI: InChI=1S/NO3/c2-1(3)4/q-1

InChIKey: InChIKey=NHNBFGGVMKEFGY-UHFFFAOYSA-N

Unification Links: CAS:14797-55-8 , ChEBI:17632 , ChemSpider:918 , HMDB:HMDB02878 , IAF1260:50426 , KEGG:C00244 , PubChem:943 , Wikipedia:Nitrate

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -26.92206 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

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

Not in pathways:
nitrate[periplasmic space] + an ubiquinol[inner membrane] → nitrite[periplasmic space] + an ubiquinone[inner membrane] + H2O[periplasmic space]

Reactions known to produce the compound:

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:
2 nitric oxide + NAD(P)H + 2 oxygen → 2 nitrate + NAD(P)+ + H+

Reactions known to both consume and produce the compound:

nitrate reduction I (denitrification) , 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:
nitrite + NAD(P)+ + H2O = nitrate + NAD(P)H + H+
nitrite + an oxidized electron acceptor + H2O = nitrate + a reduced electron acceptor
3 nitrite + 2 H+ = 2 nitric oxide + nitrate + H2O

In Transport reactions:
nitrate[extracellular space] + ATP + H2O ↔ nitrate[cytosol] + ADP + phosphate + H+ ,
nitrate[periplasmic space] + nitrite[cytosol]nitrate[cytosol] + nitrite[periplasmic space]

In Redox half-reactions:
nitrate[in] + 10 H+[in] + 8 e- → ammonium[in] + 3 H2O[in] ,
nitrate[in] + 4 H+[in] + 3 e- → nitric oxide[in] + 2 H2O[in] ,
nitrate + 2 H+ + 2 e- → nitrite + H2O ,
nitrate[in] + 2 H+[in] + 2 e- → nitrite[in] + H2O[in] ,
nitrate[out] + 2 H+[out] + 2 e- → nitrite[out] + H2O[out]

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

Inhibitor (Competitive) of: 1,4-dihydroxy-2-naphthoyl-CoA synthase [Jiang10] , cyanase [Little87, Comment 1] , formate dehydrogenase [Axley91, Axley90, Comment 2] , formate dehydrogenase [Hopner82] , ethylnitronate monooxygenase [Francis09] , nitrite-cytochrome c oxidoreductase [Tanaka83]

Inhibitor (Noncompetitive) of: phosphoenolpyruvate mutase [Seidel94]

Inhibitor (Mechanism unknown) of: α-dehydro-β-deoxy-D-glucarate aldolase [Fish66] , glycogen phosphorylase [Chen68a, Chen68] , V-type Na+-translocating ATPase [Murata01]

Credits:
Revised 23-Dec-2012 by Caspi R , SRI International


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

Axley91: Axley MJ, Grahame DA (1991). "Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase." J Biol Chem 266(21);13731-6. PMID: 1906883

Chen68: Chen GS, Segel IH (1968). "Purification and properties of glycogen phosphorylase from Escherichia coli." Arch Biochem Biophys 1968;127(1);175-86. PMID: 4878695

Chen68a: Chen GS, Segel IH (1968). "Escherichia coli polyglucose phosphorylases." Arch Biochem Biophys 1968;127(1);164-74. PMID: 4878694

Fish66: Fish D, Blumenthal H "2-keto-3-deoxy-D-glucarate aldolase." Meth Enz 1966;9:529-534.

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

Hopner82: Hopner T, Ruschig U, Muller U, Willnow P (1982). "Formate dehydrogenase from Pseudomonas oxalaticus." Methods Enzymol 89 Pt D;531-7. PMID: 7144587

Jiang10: Jiang M, Chen M, Guo ZF, Guo Z (2010). "A bicarbonate cofactor modulates 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase in menaquinone biosynthesis of Escherichia coli." J Biol Chem 285(39);30159-69. PMID: 20643650

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

Murata01: Murata T, Kawano M, Igarashi K, Yamato I, Kakinuma Y (2001). "Catalytic properties of Na(+)-translocating V-ATPase in Enterococcus hirae." Biochim Biophys Acta 1505(1);75-81. PMID: 11248190

Seidel94: Seidel HM, Knowles JR (1994). "Interaction of inhibitors with phosphoenolpyruvate mutase: implications for the reaction mechanism and the nature of the active site." Biochemistry 33(18);5641-6. PMID: 8180189

Tanaka83: Tanaka, Y., Fukumori, Y., Yamanaka, T. "Purification of cytochrome a1c1 from Nitrobacter agilis and characterization of nitrite oxidation system of the bacterium." Arch. Microbiol. 1983;135:265-271.


Report Errors or Provide Feedback
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 Mon Dec 22, 2014, biocyc11.