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2-Isopropylmalic acid (YMDB00106)

Identification
YMDB IDYMDB00106
Name2-Isopropylmalic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description2-Isopropylmalic acid is an alpha-hydroxy organic acid and is an intermediate of luecine biosynthesis. Yeast cells naturally secret this compound into their surrounding. It is thought that 2-Isopropylmalic acid secretion chelates aluminum ions and prevents them from entering cells, resulting in aluminum tolerance. [PMID: 17916978]
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • (2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid
  • (2S)-2-Hydroxy-2-isopropylsuccinic acid
  • (2S)-2-Isopropylmalate
  • (3S)-3-carboxy-3-hydroxy-4-methylpentanoic acid
  • (3S)-3-carboxy-3-hydroxyisocaproic acid
  • 2-Hydroxy-2-isopropylsuccinate
  • 2-Hydroxy-2-isopropylsuccinic acid
  • 2-Isopropyl-2-hydroxybutanedioate
  • 2-Isopropyl-2-hydroxybutanedioic acid
  • 2-isopropyl-Malic acid
  • 2-Isopropylmalate
  • 2-Isopropylmalic acid
  • 3-Carboxy-3-hydroxy-4-methylpentanoate
  • 3-Carboxy-3-hydroxyisocaproate
  • 3-Carboxy-3-hydroxyisocaproic acid
  • 3-hydroxy-4-methyl-3-carboxypentanoate
  • a-Isopropylmalate
  • a-Isopropylmalic acid
  • alpha-Isopropylmalate
  • alpha-Isopropylmalic acid
  • (S)-2-Hydroxy-2-(isopropyl)succinic acid
  • (2S)-2-Hydroxy-2-isopropylsuccinate
  • (2S)-2-Isopropylmalic acid
  • (3S)-3-Carboxy-3-hydroxy-4-methylpentanoate
  • (3S)-3-Carboxy-3-hydroxyisocaproate
  • (S)-2-Hydroxy-2-(isopropyl)succinate
  • 3-Carboxy-3-hydroxy-4-methylpentanoic acid
CAS number49601-06-1
WeightAverage: 176.1672
Monoisotopic: 176.068473494
InChI KeyBITYXLXUCSKTJS-ZETCQYMHSA-N
InChIInChI=1S/C7H12O5/c1-4(2)7(12,6(10)11)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)/t7-/m0/s1
IUPAC Name(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid
Traditional IUPAC Name2-isopropyl-malic acid
Chemical FormulaC7H12O5
SMILES[H]OC(=O)C([H])([H])[C@@](O[H])(C(=O)O[H])C([H])(C([H])([H])[H])C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Short-chain hydroxy acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Dicarboxylic acid or derivatives
  • Hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point144-146 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility181 g/LALOGPS
logP-0.29ALOGPS
logP0.21ChemAxon
logS0.01ALOGPS
pKa (Strongest Acidic)3.63ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity38.58 m³·mol⁻¹ChemAxon
Polarizability16.37 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Leucine BiosynthesisPW002475 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyruvate metabolismPW002447 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyruvate metabolismec00620 Map00620
Valine, leucine and isoleucine biosynthesisec00290 Map00290
SMPDB Reactions
2-Isopropylmalic acid + Coenzyme A ↔ Acetyl-CoA + water + Alpha-Ketoisovaleric acid
(S)-3-methyl-2-oxovaleric acid + water + Acetyl-CoA → Coenzyme A + hydron + 2-Isopropylmalic acid
2-Isopropylmalic acid → water + 2-Isopropylmaleic acid
KEGG Reactions
water + 2-Isopropylmaleic acid ↔ 2-Isopropylmalic acid
Acetyl-CoA + Alpha-Ketoisovaleric acid + water → 2-Isopropylmalic acid + hydron + Coenzyme A
Concentrations
Intracellular ConcentrationsNot Available
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
  • Kobayashi, A., Edo, H., Furihata, K., Yoshimura, E. (2005). "Secretion of an aluminum chelator, 2-isopropylmalic acid, by the budding yeast, Saccharomyces cerevisiae." J Inorg Biochem 99:1260-1263.15833351
  • Yannai S. Dictionary of food compounds with CD-ROM: additives, flavors, and ingredients. Chapman & Hall/CRC; 2004.
  • Chang, L. F., Cunningham, T. S., Gatzek, P. R., Chen, W. J., Kohlhaw, G. B. (1984). "Cloning and characterization of yeast Leu4, one of two genes responsible for alpha-isopropylmalate synthesis." Genetics 108:91-106.6090272
  • Suzuki, T., Tamura, S., Nakanishi, H., Tashiro, M., Nishizawa, N. K., Yoshimura, E. (2007). "Reduction of aluminum toxicity by 2-isopropylmalic acid in the budding yeast Saccharomyces cerevisiae." Biol Trace Elem Res 120:257-263.17916978
  • 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:Schloss J V; Magolda R; Emptage M Synthesis of alpha-isopropylmalate, beta-isopropylmalate, and dimethylcitraconate. Methods in enzymology (1988), 166 92-6.
External Links:
ResourceLink
CHEBI ID35128
HMDB IDHMDB00402
Pubchem Compound ID5280523
Kegg IDC02504
ChemSpider ID4444155
FOODB IDFDB011983
Wikipedia IDIsopropylmalic acid
BioCyc IDNot Available

Enzymes

Protein Details
1. 2-isopropylmalate synthase 2, mitochondrial
General function:
Involved in 2-isopropylmalate synthase activity
Specific function:
Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). Redundant to LEU4, responsible of about 20% of alpha-IPMS activity. Involved in leucine synthesis
Gene Name:
LEU9
Uniprot ID:
Q12166
Molecular weight:
67199.60156
Reactions
Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O → (2S)-2-isopropylmalate + CoA.
Protein Details
2. 2-isopropylmalate synthase
General function:
Involved in 2-isopropylmalate synthase activity
Specific function:
Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
Gene Name:
LEU4
Uniprot ID:
P06208
Molecular weight:
68408.29688
Reactions
Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O → (2S)-2-isopropylmalate + CoA.
Protein Details
3. 3-isopropylmalate dehydratase
General function:
Involved in 3-isopropylmalate dehydratase activity
Specific function:
Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
Gene Name:
LEU1
Uniprot ID:
P07264
Molecular weight:
85793.70313
Reactions
(2R,3S)-3-isopropylmalate → (2S)-2-isopropylmaleate + H(2)O.
(2S)-2-isopropylmaleate + H(2)O → (2S)-2-isopropylmalate.