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Identification
YMDB IDYMDB00026
NameIsocitric acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionIsocitric acid is a protonated form of isocitrate, which is a substrate of the citric acid cycle. Isocitrate is formed from citrate with the help of the enzyme aconitase, and is acted upon by isocitrate dehydrogenase. Salts and esters of isocitric acid are known as isocitrates. [Wikipedia]
Structure
Thumb
Synonyms
  • (1S,2S)-1-Hydroxypropane-1,2,3-tricarboxylate
  • 1-Hydroxy-1,2,3-propanetricarboxylate
  • 1-Hydroxy-1,2,3-propanetricarboxylic acid
  • 1-Hydroxypropane-1,2,3-tricarboxylate
  • 1-Hydroxypropane-1,2,3-tricarboxylic acid
  • 1-Hydroxytricarballylate
  • 1-Hydroxytricarballylic acid
  • 3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylate
  • 3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylic acid
  • 3-carboxy-2,3-dideoxy-Pentarate
  • 3-carboxy-2,3-dideoxy-Pentaric acid
  • D-erythro-Isocitric acid
  • D-isocitrate
  • I-CIT
  • isocitrate
  • Isocitric acid, (11)C-labeled
  • Isocitric acid, calcium salt
  • Isocitric acid, disodium salt
  • Isocitric acid, potassium salt
  • Isocitric acid, sodium salt
  • Isocitric acid, trisodium salt
  • threo-d(s)-iso-citrate
  • threo-Ds-isocitrate
CAS number320-77-4
WeightAverage: 192.1235
Monoisotopic: 192.02700261
InChI KeyODBLHEXUDAPZAU-UHFFFAOYSA-N
InChIInChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)
IUPAC Name1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional IUPAC Nameisocitric acid
Chemical FormulaC6H8O7
SMILES[H]OC(=O)C([H])([H])C([H])(C(=O)O[H])C([H])(O[H])C(=O)O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Beta-hydroxy acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • 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 point162-165 °C
Experimental Properties
PropertyValueReference
Water Solubility466 mg/mL [HMP experimental]PhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility52.5 g/LALOGPS
logP-0.35ALOGPS
logP-1.4ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)3.07ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity35.72 m³·mol⁻¹ChemAxon
Polarizability15.55 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytopasm
  • Mitochondrion
  • Peroxisome
Organoleptic PropertiesNot Available
SMPDB Pathways
Citric Acid CyclePW000952 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid Cycle 1434561204PW000970 ThumbThumb?image type=greyscaleThumb?image type=simple
Nitrogen metabolismPW002504 ThumbThumb?image type=greyscaleThumb?image type=simple
TCA CyclePW002377 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Citrate cycle (TCA cycle)ec00020 Map00020
Glyoxylate and dicarboxylate metabolismec00630 Map00630
Nitrogen metabolismec00910 Map00910
SMPDB Reactions
Isocitric acid + NADOxoglutaric acid + Carbon dioxide + NADH + hydron
cis-aconitic acid + waterIsocitric acid
NADP + Isocitric acidCarbon dioxide + hydron + NADPH + Oxoglutaric acid
Isocitric acid + NADPCarbon dioxide + hydron + NADPH + Oxoglutaric acid
Isocitric acid + NADPCarbon dioxide + hydron + NADPH + Oxoglutaric acid
KEGG Reactions
cis-aconitic acid + waterIsocitric acid
NAD + Isocitric acidNADH + Oxoglutaric acid + Carbon dioxide
NADP + Isocitric acidOxoglutaric acid + Carbon dioxide + NADPH
Isocitric acidGlyoxylic acid + Succinic acid
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
  • 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
  • Lin, A. P., Hakala, K. W., Weintraub, S. T., McAlister-Henn, L. (2008). "Suppression of metabolic defects of yeast isocitrate dehydrogenase and aconitase mutants by loss of citrate synthase." Arch Biochem Biophys 474:205-212.18359281
  • Lin, A. P., McAlister-Henn, L. (2002). "Isocitrate binding at two functionally distinct sites in yeast NAD+-specific isocitrate dehydrogenase." J Biol Chem 277:22475-22483.11953438
  • Takada, Y., Noguchi, T. (1985). "Characteristics of alanine: glyoxylate aminotransferase from Saccharomyces cerevisiae, a regulatory enzyme in the glyoxylate pathway of glycine and serine biosynthesis from tricarboxylic acid-cycle intermediates." Biochem J 231:157-163.3933486
  • Przybyla-Zawislak, B., Gadde, D. M., Ducharme, K., McCammon, M. T. (1999). "Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes." Genetics 152:153-166.10224250
  • Minard, K. I., Jennings, G. T., Loftus, T. M., Xuan, D., McAlister-Henn, L. (1998). "Sources of NADPH and expression of mammalian NADP+-specific isocitrate dehydrogenases in Saccharomyces cerevisiae." J Biol Chem 273:31486-31493.9813062
  • Cupp, J. R., McAlister-Henn, L. (1992). "Cloning and characterization of the gene encoding the IDH1 subunit of NAD(+)-dependent isocitrate dehydrogenase from Saccharomyces cerevisiae." J Biol Chem 267:16417-16423.1644826
  • 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:Finogenova, T. V.; Kamzolova, S. V.; Dedyukhina, E. G.; Shishkanova, N. V.; Il'chenko, A. P.; Morgunov, I. G.; Chernyavskaya, O. G.; Sokolov, A. P. Biosynthesis of citric and isocitric acids from ethanol by mutant Yarrowia lipolytica N 1 under continuous
External Links:
ResourceLink
CHEBI ID30887
HMDB IDHMDB00193
Pubchem Compound ID1198
Kegg IDC00311
ChemSpider ID1161
FOODB IDFDB003281
WikipediaIsocitric_acid
BioCyc IDthreo-d(s)-iso-citrate

Enzymes

General function:
Involved in metabolic process
Specific function:
Required for growth on nonfermentable carbon sources and for biosynthesis of glutamate
Gene Name:
ACO1
Uniprot ID:
P19414
Molecular weight:
85367.5
Reactions
Citrate → isocitrate.
General function:
Involved in metabolic process
Specific function:
Citrate = isocitrate
Gene Name:
ACO2
Uniprot ID:
P39533
Molecular weight:
86582.5
Reactions
Citrate → isocitrate.
General function:
Involved in isocitrate lyase activity
Specific function:
Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2- methylisocitrate
Gene Name:
ICL1
Uniprot ID:
P28240
Molecular weight:
62408.30078
Reactions
Isocitrate → succinate + glyoxylate.
General function:
Involved in magnesium ion binding
Specific function:
Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'- untranslated leaders of mitochondrial mRNAs
Gene Name:
IDH1
Uniprot ID:
P28834
Molecular weight:
39323.69922
Reactions
Isocitrate + NAD(+) → 2-oxoglutarate + CO(2) + NADH.
General function:
Involved in magnesium ion binding
Specific function:
Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'- untranslated leaders of mitochondrial mRNAs
Gene Name:
IDH2
Uniprot ID:
P28241
Molecular weight:
39739.0
Reactions
Isocitrate + NAD(+) → 2-oxoglutarate + CO(2) + NADH.
General function:
Involved in magnesium ion binding
Specific function:
May function in the production of NADPH for fatty acid and sterol synthesis
Gene Name:
IDP3
Uniprot ID:
P53982
Molecular weight:
47856.0
Reactions
Isocitrate + NADP(+) → 2-oxoglutarate + CO(2) + NADPH.
Oxalosuccinate + NADP(+) → 2-oxoglutarate + CO(2) + NADPH.
General function:
Involved in magnesium ion binding
Specific function:
Mitochondrial IDP1 may regulate flux through the tricarboxylic acid cycle and respiration. Its probably critical function is the production of NADPH
Gene Name:
IDP1
Uniprot ID:
P21954
Molecular weight:
48189.89844
Reactions
Isocitrate + NADP(+) → 2-oxoglutarate + CO(2) + NADPH.
Oxalosuccinate + NADP(+) → 2-oxoglutarate + CO(2) + NADPH.
General function:
Involved in magnesium ion binding
Specific function:
May function in the production of NADPH for fatty acid and sterol synthesis
Gene Name:
IDP2
Uniprot ID:
P41939
Molecular weight:
46561.89844
Reactions
Isocitrate + NADP(+) → 2-oxoglutarate + CO(2) + NADPH.
Oxalosuccinate + NADP(+) → 2-oxoglutarate + CO(2) + NADPH.
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the NAD(+)-dependent conversion of homoisocitrate to alpha-ketoadipate
Gene Name:
LYS12
Uniprot ID:
P40495
Molecular weight:
40068.60156
Reactions
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD(+) → 2-oxoadipate + CO(2) + NADH.
General function:
Involved in metabolic process
Specific function:
Responsible for the dehydration of cis-homoaconitate to homoisocitric acid
Gene Name:
LYS4
Uniprot ID:
P49367
Molecular weight:
75150.10156
Reactions
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate → (Z)-but-1-ene-1,2,4-tricarboxylate + H(2)O.

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