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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: citrate

Synonyms: citr, cit, citric acid, 2-hydroxy-1,2,3-propanetricarboxylic acid

Component of: sodium citrate trihydrate

Chemical Formula: C6H5O7

Molecular Weight: 189.1 Daltons

Monoisotopic Molecular Weight: 192.0270026115 Daltons

pKa 1: 3.13

pKa 2: 4.76

pKa 3: 6.39

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

InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3

InChIKey: InChIKey=KRKNYBCHXYNGOX-UHFFFAOYSA-K

Unification Links: CAS:77-92-9 , ChEBI:16947 , ChemSpider:29081 , HMDB:HMDB00094 , IAF1260:34080 , KEGG:C00158 , KNApSAcK:C00007619 , MetaboLights:MTBLC16947 , PubChem:31348

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -230.69292 Inferred by computational analysis [Latendresse, 2013]

Reactions known to consume the compound:

acetyl-CoA biosynthesis III (from citrate) , reductive TCA cycle I :
oxaloacetate + acetyl-CoA + ADP + phosphate ← citrate + ATP + coenzyme A

achromobactin biosynthesis :
citrate + ATP + ethanolamine → O-citryl-ethanolamine + AMP + diphosphate
citrate + ATP + L-serine → O-citryl-L-serine + AMP + diphosphate

aerobactin biosynthesis :
N6-acetyl-N6-hydroxy-L-lysine + citrate + 2 ATP + H2O → N1-citryl-N6-acetyl-N6-hydroxy-L-lysine + 2 ADP + 2 phosphate + 2 H+

citrate degradation :
citrate + an acetyl-[holo citrate lyase acyl-carrier protein] → a citryl-[holo citrate lyase acyl-carrier protein] + acetate

petrobactin biosynthesis :
spermidine + citrate + ATP → N-citryl-spermidine + AMP + diphosphate + H+

reductive TCA cycle II :
citrate + ATP + coenzyme A → (3S)-citryl-CoA + ADP + phosphate

rhizobactin 1021 biosynthesis :
2 N4-acetyl-N4-hydroxy-1-aminopropane + citrate → rhizobactin 1021 core + 2 H2O

Not in pathways:
ATP + citrate + L-glutamate → ADP + β-citryl-L-glutamate + phosphate + H+
citrate → acetate + oxaloacetate

Reactions known to produce the compound:

ethylene biosynthesis V (engineered) , glutamine biosynthesis III , glyoxylate cycle , itaconate biosynthesis , methylaspartate cycle , mixed acid fermentation , TCA cycle I (prokaryotic) , TCA cycle II (plants and fungi) , TCA cycle III (animals) , TCA cycle IV (2-oxoglutarate decarboxylase) , TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) , TCA cycle VI (obligate autotrophs) , TCA cycle VII (acetate-producers) , TCA cycle VIII (helicobacter) :
oxaloacetate + acetyl-CoA + H2O → citrate + coenzyme A + H+

Reactions known to both consume and produce the compound:

ethylene biosynthesis V (engineered) , glutamine biosynthesis III , glyoxylate cycle , itaconate biosynthesis , methylaspartate cycle , mixed acid fermentation , reductive TCA cycle I , reductive TCA cycle II , TCA cycle I (prokaryotic) , TCA cycle II (plants and fungi) , TCA cycle III (animals) , TCA cycle IV (2-oxoglutarate decarboxylase) , TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) , TCA cycle VI (obligate autotrophs) , TCA cycle VII (acetate-producers) , TCA cycle VIII (helicobacter) :
citrate[mitochondrial lumen]cis-aconitate[mitochondrial lumen] + H2O[mitochondrial lumen]

In Reactions of unknown directionality:

Not in pathways:
oxaloacetate + acetyl-CoA + H2O = citrate + coenzyme A + H+
citrate = D-threo-isocitrate
acetyl-CoA + citrate = acetate + (3S)-citryl-CoA

In Transport reactions:
succinate[cytosol] + citrate[periplasmic space]citrate[cytosol] + succinate[periplasmic space]

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

Activator (Allosteric) of: 6-phosphofructokinase [Garland, 1980a]

Activator (Mechanism unknown) of: fructose bisphosphate aldolase , cellobiose 2-epimerase [Taguchi08] , isoflavone-7-O-glucoside-6''-O-malonate malonyltransferase [Hinderer86] , isoflavone-7-O-glucoside-6''-O-malonate malonylesterase [Hinderer86] , isoflavone-7-O-glucoside-6''-O-malonate malonylesterase [Hinderer86] , isoflavone-7-O-glucoside-6''-O-malonate malonylesterase [Hinderer86] , isoflavone-7-O-glucoside-6''-O-malonate malonylesterase [Hinderer86] , isoflavone-7-O-glucoside-6''-O-malonate malonylesterase [Hinderer86] , fructose-1,6-bisphosphate aldolase [Siebers, 2001]

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

Inhibitor (Competitive) of: chorismate mutase [Baldwin83] , fumarase C [Weaver96] , 2-keto-4-hydroxyglutarate aldolase , enolase [Peak94] , trehalose-6-phosphate phosphatase [Matula71]

Inhibitor (Noncompetitive) of: 2-methyleneglutarate mutase [Kung71]

Inhibitor (Mechanism unknown) of: galactarate dehydratase [Blumenthal66] , isocitrate dehydrogenase kinase [Nimmo84a] , glutamine synthetase adenylyltransferase [Ebner70, Comment 1] , pyruvate kinase [Singh98] , pyruvate kinase [Plaxton02] , glutamate dehydrogenase [Kimura77] , triose phosphate isomerase [Tomlinson79]

Inhibitor (Other types) of: aspartate ammonia-lyase


References

Baldwin83: Baldwin GS, Davidson BE (1983). "Kinetic studies on the mechanism of chorismate mutase/prephenate dehydratase from Escherichia coli K12." Biochim Biophys Acta 1983;742(2);374-83. PMID: 6337635

Blumenthal66: Blumenthal, HJ, Jepson, T "Galactarate Dehydrase." Methods in Enzymology 9:665-669 (1966).

Ebner70: Ebner E, Wolf D, Gancedo C, Elsasser S, Holzer H (1970). "ATP: glutamine synthetase adenylyltransferase from Escherichia coli B. Purification and properties." Eur J Biochem 1970;14(3);535-44. PMID: 4920894

Garland, 1980a: Garland WJ, Dennis DT (1980). "Plastid and cytosolic phosphofructokinases from the developing endosperm of Ricinus communis. II. Comparison of the kinetic and regulatory properties of the isoenzymes." Arch Biochem Biophys 204(1);310-7. PMID: 6448584

Hinderer86: Hinderer W, Koster J, Barz W (1986). "Purfication and properties of a specific isoflavone 7-O-glucoside-6''-malonate malonyestrase from roots of chickpea (Cicer arietinum L.)." Arch Biochem Biophys 248(2);570-8. PMID: 3740841

Kimura77: Kimura K, Miyakawa A, Imai T, Sasakawa T (1977). "Glutamate dehydrogenase from Bacillus subtilis PCI 219. I. Purification and properties." J Biochem (Tokyo) 81(2);467-76. PMID: 14949

Kung71: Kung HF, Stadtman TC (1971). "Nicotinic acid metabolism. VI. Purification and properties of alpha-methyleneglutarate mutase (B 12-dependent) and methylitaconate isomerase." J Biol Chem 246(10);3378-88. PMID: 5574401

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

Matula71: Matula M, Mitchell M, Elbein AD (1971). "Partial purification and properties of a highly specific trehalose phosphate phosphatase from Mycobacterium smegmatis." J Bacteriol 107(1);217-22. PMID: 4327508

Nimmo84a: Nimmo GA, Nimmo HG (1984). "The regulatory properties of isocitrate dehydrogenase kinase and isocitrate dehydrogenase phosphatase from Escherichia coli ML308 and the roles of these activities in the control of isocitrate dehydrogenase." Eur J Biochem 1984;141(2);409-14. PMID: 6329757

Peak94: Peak MJ, Peak JG, Stevens FJ, Blamey J, Mai X, Zhou ZH, Adams MW (1994). "The hyperthermophilic glycolytic enzyme enolase in the archaeon, Pyrococcus furiosus: comparison with mesophilic enolases." Arch Biochem Biophys 313(2);280-6. PMID: 8080274

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

Siebers, 2001: Siebers B, Brinkmann H, Dorr C, Tjaden B, Lilie H, van der Oost J, Verhees CH (2001). "Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase." J Biol Chem 276(31);28710-8. PMID: 11387336

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

Taguchi08: Taguchi H, Hamada S, Kawauchi S, Ito H, Senoura T, Watanabe J, Nishimukai M, Ito S, Matsui H (2008). "Enzymatic properties of cellobiose 2-epimerase from Ruminococcus albus and the synthesis of rare oligosaccharides by the enzyme." Appl Microbiol Biotechnol 79(3);433-41. PMID: 18392616

Tomlinson79: Tomlinson J.D., Turner J.F. "Pea seed triose phosphate isomerase." Phytochemistry (1979) 18:1959-1962.

Weaver96: Weaver T, Banaszak L (1996). "Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli." Biochemistry 35(44);13955-65. PMID: 8909293


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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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