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

Synonyms: oxalic acid, ethanedioic acid

Summary:
Oxalate is the most oxidized two-carbon compound. It is made in high concentrations by some plants and fungi and can reach high micromolar concentrations in soil. Oxalate is toxic to mammals but is metabolized by many bacteria and plants by various pathways. In high concentrations, it causes death in humans and animals because of its corrosive effects, while smaller amounts can cause various pathological disorders, including hyperoxaluria, calcium oxalate stones, pyridoxine deficiency, and even renal failure.

Chemical Formula: C2O4

Molecular Weight: 88.02 Daltons

Monoisotopic Molecular Weight: 89.9953085526 Daltons

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

InChI: InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-2

InChIKey: InChIKey=MUBZPKHOEPUJKR-UHFFFAOYSA-L

Unification Links: CAS:144-62-7 , ChEBI:30623 , ChemSpider:64235 , HMDB:HMDB02329 , KEGG:C00209 , MetaboLights:MTBLC30623 , PubChem:71081

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -162.34824 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

oxalate degradation I :
oxalate + an oxidized ferredoxin → 2 CO2 + a reduced ferredoxin

oxalate degradation II :
formate[in] + oxalate[out] → formate[out] + oxalate[in]
formyl-CoA + oxalate → formate + oxalyl-CoA
oxalate + succinyl-CoA → oxalyl-CoA + succinate

oxalate degradation III :
oxalate + succinyl-CoA → oxalyl-CoA + succinate

oxalate degradation IV :
oxalate + oxygen + 2 H+ → 2 CO2 + hydrogen peroxide

Not in pathways:
oxalate + ATP + coenzyme A → oxalyl-CoA + AMP + diphosphate

Reactions known to produce the compound:

factor 420 biosynthesis :
5-amino-6-(D-ribitylamino)uracil + 4-hydroxyphenylpyruvate + 2 S-adenosyl-L-methionine + H2O → 7,8-didemethyl-8-hydroxy-5-deazariboflavin + 2 5'-deoxyadenosine + 2 L-methionine + oxalate + ammonium + 3 H+

L-ascorbate degradation III :
4-O-oxalyl-L-threonate + H2O → L-threonate + oxalate + H+

oxalate biosynthesis :
oxaloacetate + H2O → oxalate + acetate + H+

trichloroethylene degradation :
dichloroacetate → oxalate
trichloroacetate + 2 H2O → oxalate + 3 chloride + 4 H+

Not in pathways:
glyoxylate + oxygen + H2O → hydrogen peroxide + oxalate + H+

In Reactions of unknown directionality:

oxalate degradation V :
oxalate + H+ = formate + CO2

Not in pathways:
oxamate + H2O = oxalate + ammonium
acetyl-CoA + oxalate = oxalyl-CoA + acetate

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

Activator (Mechanism unknown) of: NAD+-dependent malate dehydrogenase [Park89]

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

Inhibitor (Competitive) of: malate synthase G [Falmagne65] , isocitrate lyase [Comment 1] , glutamate decarboxylase A [Fonda72] , glutamate decarboxylase B [Fonda72] , D-lactate dehydrogenase [Kaczorowski78] , cyanase [Anderson87, Comment 2] , phosphoenolpyruvate mutase [Seidel94] , 3-phosphonopyruvate hydrolase [Chen06a] , pyruvate kinase [Singh98] , acetylpyruvate hydrolase [Davey75]

Inhibitor (Noncompetitive) of: pyruvate kinase [Singh98]

Inhibitor (Allosteric) of: L-lactate dehydrogenase

Inhibitor (Mechanism unknown) of: 2-oxopent-4-enoate hydratase [Pollard98a] , phosphoenolpyruvate synthetase [Narindrasorasak78] , formyl-CoA transferase [Toyota08] , pH 2.5 acid phosphatase [Dassa82, Comment 3] , NAD+-dependent malate dehydrogenase [Kiick86] , pyruvate kinase [Plaxton02] , pyruvate kinase [Smith00] , L-lactate dehydrogenase [Davies72] , malate synthase [Smith03] , isocitrate lyase [Honer99]

Credits:
Revised 20-Jan-2011 by Caspi R , SRI International


References

Anderson87: Anderson PM, Johnson WV, Endrizzi JA, Little RM, Korte JJ (1987). "Interaction of mono- and dianions with cyanase: evidence for apparent half-site binding." Biochemistry 26(13);3938-43. PMID: 3651424

Chen06a: Chen CC, Han Y, Niu W, Kulakova AN, Howard A, Quinn JP, Dunaway-Mariano D, Herzberg O (2006). "Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily." Biochemistry 45(38);11491-504. PMID: 16981709

Dassa82: Dassa E, Cahu M, Desjoyaux-Cherel B, Boquet PL (1982). "The acid phosphatase with optimum pH of 2.5 of Escherichia coli. Physiological and Biochemical study." J Biol Chem 1982;257(12);6669-76. PMID: 6282821

Davey75: Davey JF, Ribbons DW (1975). "Metabolism of resorcinylic compounds by bacteria. Purification and properties of acetylpyruvate hydrolase from Pseudomonas putida 01." J Biol Chem 1975;250(10);3826-30. PMID: 236305

Davies72: Davies DD, Davies S (1972). "Purification and properties of L(+)-lactate dehydrogenase from potato tubers." Biochem J 129(4);831-9. PMID: 4144124

Falmagne65: Falmagne P, Vanderwinkel E, Wiame JM (1965). "Mise en evidence de deux malate synthases chez E. coli." BBActa 1965;99:246-258. PMID: 14336062

Fonda72: Fonda ML (1972). "Glutamate decarboxylase. Substrate specificity and inhibition by carboxylic acids." Biochemistry 1972;11(7);1304-9. PMID: 4552052

Honer99: Honer Zu Bentrup K, Miczak A, Swenson DL, Russell DG (1999). "Characterization of activity and expression of isocitrate lyase in Mycobacterium avium and Mycobacterium tuberculosis." J Bacteriol 181(23);7161-7. PMID: 10572116

Hoyt88: Hoyt JC, Robertson EF, Berlyn KA, Reeves HC (1988). "Escherichia coli isocitrate lyase: properties and comparisons." Biochim Biophys Acta 1988;966(1);30-5. PMID: 3291954

Kaczorowski78: Kaczorowski G, Kohn LD, Kaback HR (1978). "Purification and properties of D-lactate dehydrogenase from Escherichia coli ML 308-225." Methods Enzymol 1978;53;519-27. PMID: 362128

Kiick86: Kiick DM, Harris BG, Cook PF (1986). "Protonation mechanism and location of rate-determining steps for the Ascaris suum nicotinamide adenine dinucleotide-malic enzyme reaction from isotope effects and pH studies." Biochemistry 25(1);227-36. PMID: 3513825

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

Narindrasorasak78: Narindrasorasak S, Bridger WA (1978). "Probes of the structure of phosphoenolpyruvate synthetase: effects of a transition state analogue on enzyme conformation." Can J Biochem 56(8);816-9. PMID: 210911

Park89: Park SH, Harris BG, Cook PF (1989). "Substrate activation by malate induced by oxalate in the Ascaris suum NAD-malic enzyme reaction." Biochemistry 28(15);6334-40. PMID: 2790001

Plaxton02: Plaxton WC, Smith CR, Knowles VL (2002). "Molecular and regulatory properties of leucoplast pyruvate kinase from Brassica napus (rapeseed) suspension cells." Arch Biochem Biophys 400(1);54-62. PMID: 11913971

Pollard98a: Pollard JR, Bugg TD (1998). "Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli." Eur J Biochem 251(1-2);98-106. PMID: 9492273

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

Singh98: Singh DK, Malhotra SP, Singh R (1998). "Purification and characterizaton of plastidic pyruvate kinase from developing seeds of Brassica campestris L." Indian J Biochem Biophys 35(6);346-52. PMID: 10412228

Smith00: Smith CR, Knowles VL, Plaxton WC (2000). "Purification and characterization of cytosolic pyruvate kinase from Brassica napus (rapeseed) suspension cell cultures: implications for the integration of glycolysis with nitrogen assimilation." Eur J Biochem 267(14);4477-85. PMID: 10880971

Smith03: Smith CV, Huang CC, Miczak A, Russell DG, Sacchettini JC, Honer zu Bentrup K (2003). "Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis." J Biol Chem 278(3);1735-43. PMID: 12393860

Toyota08: Toyota CG, Berthold CL, Gruez A, Jonsson S, Lindqvist Y, Cambillau C, Richards NG (2008). "Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase." J Bacteriol 190(7):2556-64. PMID: 18245280


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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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