You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00280
Name(S)-Malic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionL-Malic acid, also known as malate or L-apple acid, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. L-Malic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). L-Malic acid exists in all eukaryotes, ranging from yeast to humans.
Structure
Thumb
Synonyms
  • (-)-(S)-Malate
  • (-)-(S)-Malic acid
  • (-)-Hydroxysuccinate
  • (-)-Hydroxysuccinic acid
  • (-)-L-Malic acid
  • (-)-Malic acid
  • (2S)-2-Hydroxybutanedioate
  • (2S)-2-Hydroxybutanedioic acid
  • (S)-(-)-Hydroxysuccinate
  • (S)-(-)-Hydroxysuccinic acid
  • (S)-hydroxy-Butanedioate
  • (S)-hydroxy-Butanedioic acid
  • (S)-Hydroxybutanedioate
  • (S)-Hydroxybutanedioic acid
  • (s)-malate
  • Apple acid
  • Butanedioic acid, hydroxy-, (S)-
  • L-(-)-Malic acid
  • l-2-hydroxybutanedioic acid
  • l-apple acid
  • L-Hydroxybutanedioate
  • L-Hydroxybutanedioic acid
  • L-Hydroxysuccinate
  • L-Hydroxysuccinic acid
  • L-Malate
  • L-malic acid
  • malate
  • Malic acid
  • MLT
  • S-(-)-Malate
  • S-(-)-Malic acid
  • S-2-Hydroxybutanedioate
  • S-2-Hydroxybutanedioic acid
  • (-)-L-Malate
  • L-2-Hydroxybutanedioate
  • (S)-Malic acid
CAS number97-67-6
WeightAverage: 134.0874
Monoisotopic: 134.021523302
InChI KeyBJEPYKJPYRNKOW-REOHCLBHSA-N
InChIInChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m0/s1
IUPAC Name(2S)-2-hydroxybutanedioic acid
Traditional IUPAC Name(-)-malic acid
Chemical FormulaC4H6O5
SMILESO[C@@H](CC(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Short-chain hydroxy acid
  • Beta-hydroxy acid
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point107 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility218 g/LALOGPS
logP-0.87ALOGPS
logP-1.1ChemAxon
logS0.21ALOGPS
pKa (Strongest Acidic)3.2ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity24.88 m³·mol⁻¹ChemAxon
Polarizability10.93 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic Properties
Flavour/OdourSource
OdorlessFDB012047
SMPDB Pathways
Aspartate metabolismPW002375 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid CyclePW000952 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid Cycle 1434561204PW000970 ThumbThumb?image type=greyscaleThumb?image type=simple
Glyoxylate cyclePW002419 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyruvate metabolismPW002447 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Citrate cycle (TCA cycle)ec00020 Map00020
Glyoxylate and dicarboxylate metabolismec00630 Map00630
Methane metabolismec00680 Map00680
Pyruvate metabolismec00620 Map00620
SMPDB Reactions
(S)-Malic acidFumaric acid + water
(S)-Malic acid + NADOxalacetic acid + NADH + hydron
Oxalacetic acid + hydron + NADH(S)-Malic acid + NAD
NADH + hydron + Oxalacetic acid(S)-Malic acid + NAD
Glyoxylic acid + Acetyl-CoA + waterCoenzyme A + hydron + (S)-Malic acid
KEGG ReactionsNot Available
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
2515 ± 126 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Luttik, M. A., Kotter, P., Salomons, F. A., van der Klei, I. J., van Dijken, J. P., Pronk, J. T. (2000). "The Saccharomyces cerevisiae ICL2 gene encodes a mitochondrial 2-methylisocitrate lyase involved in propionyl-coenzyme A metabolism." J Bacteriol 182:7007-7013.11092862
  • Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666
Synthesis Reference:McKenzie, Alex.; Plenderleith, H. J.; Walker, Nellie. Optical activation of racemic acid by d-malic acid. Journal of the Chemical Society, Transactions (1923), 123 2875-80.
External Links:
ResourceLink
CHEBI ID30797
HMDB IDHMDB00156
Pubchem Compound ID222656
Kegg IDC00149
ChemSpider ID193317
FOODB IDFDB012047
WikipediaMalic_acid
BioCyc IDMAL

Enzymes

General function:
Involved in catalytic activity
Specific function:
This isozyme is necessary for growth on acetate as sole C-source
Gene Name:
MLS1
Uniprot ID:
P30952
Molecular weight:
62790.60156
Reactions
Acetyl-CoA + H(2)O + glyoxylate → (S)-malate + CoA.
General function:
Involved in catalytic activity
Specific function:
This isozyme is involved in the degradation of allantoin (purine catabolism)
Gene Name:
DAL7
Uniprot ID:
P21826
Molecular weight:
62793.39844
Reactions
Acetyl-CoA + H(2)O + glyoxylate → (S)-malate + CoA.
General function:
Involved in fumarate hydratase activity
Specific function:
(S)-malate = fumarate + H(2)O
Gene Name:
FUM1
Uniprot ID:
P08417
Molecular weight:
53151.5
Reactions
(S)-malate → fumarate + H(2)O.
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
The isoenzyme MDH2 may function primarily in the glyoxylate cycle
Gene Name:
MDH2
Uniprot ID:
P22133
Molecular weight:
40730.39844
Reactions
(S)-malate + NAD(+) → oxaloacetate + NADH.
General function:
Involved in oxidoreductase activity
Specific function:
(S)-malate + NAD(+) = pyruvate + CO(2) + NADH
Gene Name:
MAE1
Uniprot ID:
P36013
Molecular weight:
74375.29688
Reactions
(S)-malate + NAD(+) → pyruvate + CO(2) + NADH.
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
(S)-malate + NAD(+) = oxaloacetate + NADH
Gene Name:
MDH3
Uniprot ID:
P32419
Molecular weight:
37185.89844
Reactions
(S)-malate + NAD(+) → oxaloacetate + NADH.
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
(S)-malate + NAD(+) = oxaloacetate + NADH
Gene Name:
MDH1
Uniprot ID:
P17505
Molecular weight:
35649.60156
Reactions
(S)-malate + NAD(+) → oxaloacetate + NADH.

Transporters

General function:
Involved in binding
Specific function:
Transport of citrate across inner mitochondrial membrane
Gene Name:
CTP1
Uniprot ID:
P38152
Molecular weight:
32173.0
General function:
Involved in antiporter activity
Specific function:
Mitochondrial dicarboxylic transporter catalyzing the exchange of dicarboxylic acids like malate and succinate for inorganic phosphate. Required for growth on ethanol and acetate
Gene Name:
DIC1
Uniprot ID:
Q06143
Molecular weight:
32991.30078