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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: (S)-malate

Synonyms: (S)-malic acid, L-apple acid, L-malic acid, L-hydroxysuccinic acid, L-hydroxybutanedioic acid, L-malate

Superclasses: an acid all carboxy acids a carboxylate a dicarboxylate a C4-dicarboxylate (RS)-malate

Chemical Formula: C4H4O5

Molecular Weight: 132.07 Daltons

Monoisotopic Molecular Weight: 134.0215233031 Daltons

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

InChI: InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2/t2-/m0/s1

InChIKey: InChIKey=BJEPYKJPYRNKOW-REOHCLBHSA-L

Unification Links: CAS:97-67-6 , CAS:6915-15-7 , ChEBI:15589 , ChemSpider:4573566 , HMDB:HMDB00156 , IAF1260:34045 , KEGG:C00149 , MetaboLights:MTBLC15589 , PubChem:5459792

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -161.16376 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

anaerobic energy metabolism (invertebrates, mitochondrial) , C4 photosynthetic carbon assimilation cycle, NAD-ME type , chitin degradation to ethanol , L-carnitine degradation III :
(S)-malate + NAD+ → pyruvate + CO2 + NADH

bacillithiol biosynthesis :
UDP-N-acetyl-α-D-glucosamine + (S)-malate → malyl-N-acetyl-D-glucosamine + UDP + H+

C4 photosynthetic carbon assimilation cycle, NADP-ME type , C4 photosynthetic carbon assimilation cycle, PEPCK type :
(S)-malate + NADP+ → CO2 + pyruvate + NADPH

gluconeogenesis I :
(S)-malate + NAD+ → pyruvate + CO2 + NADH
(S)-malate + NADP+ → CO2 + pyruvate + NADPH

phaselate biosynthesis :
caffeoyl-CoA + (S)-malate → phaselate + coenzyme A

sinapate ester biosynthesis :
(S)-malate + 1-O-sinapoyl-β-D-glucose → sinapoyl-(S)-malate + β-D-glucose

TCA cycle I (prokaryotic) , TCA cycle VII (acetate-producers) :
(S)-malate + a quinone → oxaloacetate + a quinol

TCA cycle VIII (helicobacter) :
(S)-malate + a menaquinone → oxaloacetate + a menaquinol

methyl ketone biosynthesis :
a carboxylate + ATP + coenzyme A → an acyl-CoA + AMP + diphosphate

Not in pathways:
an acyl-protein synthetase + a carboxylate + ATP → an acyl-protein thioester + AMP + diphosphate
a carboxylate + GTP + coenzyme A → an acyl-CoA + GDP + phosphate

Reactions known to produce the compound:

C4 photosynthetic carbon assimilation cycle, NADP-ME type , C4 photosynthetic carbon assimilation cycle, PEPCK type :
(S)-malate + NADP+ ← oxaloacetate + NADPH + H+

chitin degradation to ethanol , glycolate and glyoxylate degradation II , glyoxylate cycle , L-arabinose degradation IV , methylaspartate cycle , TCA cycle IV (2-oxoglutarate decarboxylase) , TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) , xylose degradation IV :
acetyl-CoA + glyoxylate + H2O → (S)-malate + coenzyme A + H+

L-carnitine degradation III :
L-malic semialdehyde + NAD(P)+ + H2O → (S)-malate + NAD(P)H + 2 H+

Not in pathways:
(S)-malyl-CoA + H2O → (S)-malate + coenzyme A + H+

3,3'-thiodipropionate degradation :
3-sulfinopropionate + an acyl-CoA → 3-sulfinopropanoyl-CoA + a carboxylate

dimethylsulfoniopropionate degradation II (cleavage) :
dimethylsulfoniopropanoate + an acyl-CoA → dimethylsulfoniopropioyl-CoA + a carboxylate

NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) :
an aldehyde + NADP+ + H2O → a carboxylate + NADPH + 2 H+
an aldehyde + NAD+ + H2O → a carboxylate + NADH + 2 H+

phosphatidylcholine resynthesis via glycerophosphocholine :
a phosphatidylcholine + 2 H2O → sn-glycero-3-phosphocholine + 2 a carboxylate + 2 H+


an acyl-CoA + H2O → a carboxylate + coenzyme A + H+
an L-1-phosphatidyl-inositol + H2O → 1-acyl-sn-glycero-3-phospho-D-myo-inositol + a carboxylate + H+
a carboxylic ester + H2O → an alcohol + a carboxylate + H+
an aldehyde + oxygen + H2O → a carboxylate + hydrogen peroxide + H+
a 1-lysophosphatidylcholine[periplasmic space] + H2O[periplasmic space]a carboxylate[periplasmic space] + sn-glycero-3-phosphocholine[periplasmic space] + H+[periplasmic space]
an aldehyde + FMNH2 + oxygen → hν + a carboxylate + FMN + H2O + 2 H+
an acylcholine + H2O → choline + a carboxylate + H+
a 1,2-diacyl-3-β-D-galactosyl-sn-glycerol + 2 H2O → 2 a carboxylate + 3-β-D-galactosyl-sn-glycerol + 2 H+
an acyl phosphate + H2O → a carboxylate + phosphate + H+
an S-acylglutathione + H2O → a carboxylate + glutathione
an N-acyl-L-aspartate + H2O → L-aspartate + a carboxylate

Reactions known to both consume and produce the compound:

3-hydroxypropanoate cycle :
succinyl-CoA + (S)-malate ↔ succinate + (S)-malyl-CoA

anaerobic energy metabolism (invertebrates, cytosol) , aspartate degradation II , C4 photosynthetic carbon assimilation cycle, NAD-ME type , gluconeogenesis I , gluconeogenesis III , glyoxylate cycle :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+

anaerobic energy metabolism (invertebrates, mitochondrial) , TCA cycle VII (acetate-producers) , TCA cycle VIII (helicobacter) :
(S)-malate ↔ fumarate + H2O

ethylmalonyl pathway :
(S)-malate + ATP + coenzyme A ↔ (S)-malyl-CoA + ADP + phosphate

formaldehyde assimilation I (serine pathway) :
(S)-malate + ATP + coenzyme A ↔ (S)-malyl-CoA + ADP + phosphate
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+

incomplete reductive TCA cycle :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

methylaspartate cycle :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

mixed acid fermentation :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

pyruvate fermentation to propionate I :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

reductive TCA cycle I :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

reductive TCA cycle II :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

superpathway of glyoxylate cycle and fatty acid degradation :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

TCA cycle I (prokaryotic) :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

TCA cycle II (plants and fungi) :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

TCA cycle III (animals) :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

TCA cycle IV (2-oxoglutarate decarboxylase) :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

TCA cycle VI (obligate autotrophs) :
(S)-malate + NAD+ ↔ oxaloacetate + NADH + H+
(S)-malate ↔ fumarate + H2O

Not in pathways:
(S)-malate + NAD(P)+ ↔ oxaloacetate + NAD(P)H + H+

sphingolipid recycling and degradation (yeast) :
a dihydroceramide + H2O ↔ sphinganine + a carboxylate

In Reactions of unknown directionality:

Not in pathways:
(S)-lactate + oxaloacetate = pyruvate + (S)-malate


a monoamide of a dicarboxylate + H2O = ammonium + a dicarboxylate


eugenol + a carboxylate + NADP+ = a coniferyl ester + NADPH
a penicillin + H2O = 6-aminopenicillanate + a carboxylate
an aldehyde[periplasmic space] + FAD[periplasmic space] + H2O[periplasmic space] = a carboxylate[periplasmic space] + FADH2[periplasmic space]
an aldehyde + pyrroloquinoline quinone + H2O = a carboxylate + pyrroloquinoline quinol + H+
a nitrile + 2 H2O = a carboxylate + ammonium
an aliphatic nitrile + 2 H2O = a carboxylate + ammonium
an N-acyl-L-homoserine lactone + H2O = L-homoserine lactone + a carboxylate
an aldehyde + an oxidized electron acceptor + H2O = a carboxylate + a reduced electron acceptor + H+
an N-acylated aromatic-L-amino acid + H2O = a carboxylate + an aromatic L-amino acid
an N-acylated-D-amino acid + H2O = a D-amino acid + a carboxylate
an N-acylated aliphatic-L-amino acid + H2O = a carboxylate + an aliphatic L-amino acid
a D-hexose + an acyl phosphate = a D-hexose-phosphate + a carboxylate
an aldehyde + 2 an oxidized ferredoxin + H2O = a carboxylate + 2 a reduced ferredoxin + 3 H+
an aldehyde + NAD(P)+ + H2O = a carboxylate + NAD(P)H + 2 H+
an N-acyl-D-glutamate + H2O = a carboxylate + D-glutamate
an anilide + H2O = aniline + a carboxylate + H+
a 5'-acylphosphoadenosine + H2O = a carboxylate + AMP + 2 H+
a 3-acylpyruvate + H2O = a carboxylate + pyruvate + H+
an N6acyl-L-lysine + H2O = a carboxylate + L-lysine
an N-acyl-D-aspartate + H2O = a carboxylate + D-aspartate

In Transport reactions:
(S)-malate[chloroplast stroma](S)-malate[cytosol] ,
(S)-malate[cytosol](S)-malate[mitochondrial lumen] ,
(S)-malate[periplasmic space] + 2 H+[periplasmic space](S)-malate[cytosol] + 2 H+[cytosol] ,
succinate[cytosol] + (S)-malate[periplasmic space](S)-malate[cytosol] + succinate[periplasmic space] ,
a C4-dicarboxylate[cytosol] + 2 H+[cytosol]a C4-dicarboxylate[cytosol] + 2 H+[cytosol] ,
a C4-dicarboxylate[periplasmic space] + 3 H+[periplasmic space]a C4-dicarboxylate[cytosol] + 3 H+[cytosol]

Enzymes activated by (S)-malate, sorted by the type of activation, are:

Activator (Mechanism unknown) of: 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]

Enzymes inhibited by (S)-malate, sorted by the type of inhibition, are:

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

Inhibitor (Uncompetitive) of: malate dehydrogenase, NAD-requiring [Wang07e]

Inhibitor (Noncompetitive) of: glutamate dehydrogenase (NAD-dependent) [Bonete96, Comment 1]

Inhibitor (Allosteric) of: phosphoenolpyruvate carboxylase [Izui81] , phosphoenolpyruvate carboxylase , L-lactate dehydrogenase

Inhibitor (Mechanism unknown) of: glutamine synthetase adenylyltransferase [Ebner70] , malate synthase [Smith03] , isocitrate lyase [Honer99]


References

Bonete96: Bonete MJ, Perez-Pomares F, Ferrer J, Camacho ML (1996). "NAD-glutamate dehydrogenase from Halobacterium halobium: inhibition and activation by TCA intermediates and amino acids." Biochim Biophys Acta 1996;1289(1);14-24. PMID: 8605224

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

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

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

Izui81: Izui K, Taguchi M, Morikawa M, Katsuki H (1981). "Regulation of Escherichia coli phosphoenolpyruvate carboxylase by multiple effectors in vivo. II. Kinetic studies with a reaction system containing physiological concentrations of ligands." J Biochem 90(5);1321-31. PMID: 7040354

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

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

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

Wang07e: Wang J, Tan H, Zhao ZK (2007). "Over-expression, purification, and characterization of recombinant NAD-malic enzyme from Escherichia coli K12." Protein Expr Purif 53(1):97-103. PMID: 17215140


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 Nov 24, 2014, BIOCYC14B.