(2R)-Homocitric acid (YMDB00096)

Identification
YMDB IDYMDB00096
Name(2R)-Homocitric acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionHomocitric acid, also known as homocitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Homocitric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Homocitric acid exists in all living species, ranging from bacteria to humans. Within yeast, homocitric acid participates in a number of enzymatic reactions. In particular, homocitric acid can be biosynthesized from oxoglutaric acid and acetyl-CoA through its interaction with the enzyme homocitrate synthase, mitochondrial. In addition, homocitric acid can be biosynthesized from oxoglutaric acid and acetyl-CoA; which is mediated by the enzyme homocitrate synthase, cytosolic isozyme. In yeast, homocitric acid is involved in the metabolic pathway called the lysine metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (R)-2-Hydroxy-1,2,4-butanetricarboxylate
  • (R)-2-Hydroxy-1,2,4-butanetricarboxylic acid
  • (R)-2-Hydroxybutane-1,2,4-tricarboxylate
  • (R)-2-hydroxybutane-1,2,4-tricarboxylic acid
  • (R)-homocitric acid
  • 2-Hydroxybutane-1,2,4-tricarboxylate
  • 3-Hydroxy-3-carboxyadipate
  • 3-Hydroxy-3-carboxyadipic acid
  • Homocitrate
  • Homocitric acid
  • (R)-Homocitrate
  • (2R)-2-Hydroxy-1,2,4-butanetricarboxylate
  • (2R)-2-Hydroxy-1,2,4-butanetricarboxylic acid
  • (±)-homocitrate
  • (±)-homocitric acid
  • 2-Hydroxy-1,2,4-butanetricarboxylate
  • 2-Hydroxy-1,2,4-butanetricarboxylic acid
CAS number3562-74-1
WeightAverage: 206.1501
Monoisotopic: 206.042652674
InChI KeyXKJVEVRQMLKSMO-SSDOTTSWSA-N
InChIInChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1
IUPAC Name(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid
Traditional IUPAC Name(R)-homocitric acid
Chemical FormulaC7H10O7
SMILESOC(=O)CC[C@@](O)(CC(O)=O)C(O)=O
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
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Tertiary 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 pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility191 g/LALOGPS
logP-1.5ALOGPS
logP-1ChemAxon
logS-0.03ALOGPS
pKa (Strongest Acidic)3.09ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity40.38 m³·mol⁻¹ChemAxon
Polarizability17.44 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Mitochondrion, Nucleus
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyruvate metabolismPW002447 ThumbThumb?image type=greyscaleThumb?image type=simple
lysine metabolismPW002420 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Lysine biosynthesisec00300 Map00300
Pyruvate metabolismec00620 Map00620
SMPDB Reactions
Oxoglutaric acid + Acetyl-CoA + water → Coenzyme A + (2R)-Homocitric acid + hydron
Acetyl-CoA + water ↔ (2R)-Homocitric acid + Coenzyme A
Oxoglutaric acid + Acetyl-CoA + water → (2R)-Homocitric acid + Coenzyme A + hydron
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fsr-2900000000-1b6221744212821d13a4JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-004i-6039700000-bbcdc859874cb31d16dbJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-06ya-0910000000-10ce2a6c7dde8f6414f9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03kc-6900000000-cc774f0962c580270a86JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gb9-3900000000-1dbf32a3d216327d832aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-08fr-1910000000-24186d115834b7a98219JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-07vi-3900000000-78ce979f1c8cb053a6d2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0aor-9600000000-dc1759e8907b4db138bdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-07wl-1910000000-93d90a9e9b47624dde71JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014r-2900000000-10b9bd64cc7e5be41000JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00ku-9800000000-3926d2bdbaae25830936JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-052u-0930000000-b304c640e74bcbd68b82JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-9200000000-f4181d391bb21114c3e1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-28608fc4dea9afb51354JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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
  • Maragoudakis, M. E., Strassman, M. (1966). "Homocitric acid accumulation by a lysine-requiring yeast mutant." J Biol Chem 241:695-699.5908136
  • Strassman, M., Ceci, L. N. (1965). "Enzymatic formation of alpha-ketoadipic acid from homoisocitric acid." J Biol Chem 240:4357-4361.4284830
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID52222
HMDB IDHMDB03518
Pubchem Compound ID439459
Kegg IDC01251
ChemSpider ID388564
FOODB IDFDB023186
WikipediaHomocitrate
BioCyc IDHOMO-CIT

Enzymes

Protein Details
1. Homocitrate synthase, mitochondrial
General function:
Involved in transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer
Specific function:
Acetyl-CoA + H(2)O + 2-oxoglutarate = (R)-2- hydroxybutane-1,2,4-tricarboxylate + CoA
Gene Name:
LYS21
Uniprot ID:
Q12122
Molecular weight:
48593.80078
Reactions
Acetyl-CoA + H(2)O + 2-oxoglutarate → (R)-2-hydroxybutane-1,2,4-tricarboxylate + CoA.
Protein Details
2. Homocitrate synthase, cytosolic isozyme
General function:
Involved in transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer
Specific function:
Acetyl-CoA + H(2)O + 2-oxoglutarate = (R)-2- hydroxybutane-1,2,4-tricarboxylate + CoA
Gene Name:
LYS20
Uniprot ID:
P48570
Molecular weight:
47098.39844
Reactions
Acetyl-CoA + H(2)O + 2-oxoglutarate → (R)-2-hydroxybutane-1,2,4-tricarboxylate + CoA.
Protein Details
3. Homoaconitase, mitochondrial
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.