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 IDYMDB00033
NameGlyoxylic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlyoxylic acid, also known as a-ketoacetate or glyoxylate, belongs to the class of organic compounds known as carboxylic acids. Carboxylic acids are compounds containing a carboxylic acid group with the formula -C(=O)OH. Glyoxylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Glyoxylic acid exists in all living species, ranging from bacteria to humans. Within yeast, glyoxylic acid participates in a number of enzymatic reactions. In particular, glyoxylic acid and acetyl-CoA can be converted into L-malic acid through its interaction with the enzyme malate synthase. In addition, succinic acid and glyoxylic acid can be biosynthesized from D-threo-isocitric acid; which is catalyzed by the enzyme isocitrate lyase. In yeast, glyoxylic acid is involved in the metabolic pathway called the glyoxylate cycle pathway. Glyoxylic acid is a potentially toxic compound.
Structure
Thumb
Synonyms
  • a-Ketoacetate
  • a-Ketoacetic acid
  • acetic acid
  • Acetic acid, oxo-
  • alpha-Ketoacetate
  • alpha-Ketoacetic acid
  • Formic acid, formyl-
  • Formylformate
  • Formylformic acid
  • Glyoxalate
  • Glyoxalic acid
  • Glyoxalsaeure
  • Glyoxylat
  • Glyoxylate
  • Glyoxylic acid
  • Glyoxylic acid, 14c2-labeled
  • Glyoxylic acid, 2-(14)C-labeled
  • Glyoxylic acid, calcium salt
  • Glyoxylic acid, sodium salt
  • Glyoxylic acid, sodium salt, 14C-labeled
  • Glyoxylic acid, sodium salt, 2-(14)C-labeled
  • Glyoxylsaeure
  • Kyselina glyoxylova
  • OCHCOOH
  • Oxalaldehydate
  • Oxalaldehydic acid
  • Oxoacetate
  • Oxoacetic acid
  • Oxoethanoate
  • Oxoethanoic acid
  • α-ketoacetate
  • α-ketoacetic acid
  • Α-ketoacetate
  • Α-ketoacetic acid
CAS number298-12-4
WeightAverage: 74.0355
Monoisotopic: 74.00039393
InChI KeyHHLFWLYXYJOTON-UHFFFAOYSA-N
InChIInChI=1S/C2H2O3/c3-1-2(4)5/h1H,(H,4,5)
IUPAC Name2-oxoacetic acid
Traditional IUPAC Nameglyoxylic acid
Chemical FormulaC2H2O3
SMILES[H]OC(=O)C([H])=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as carboxylic acids. Carboxylic acids are compounds containing a carboxylic acid group with the formula -C(=O)OH.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acids
Direct ParentCarboxylic acids
Alternative Parents
Substituents
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Organooxygen compound
  • Carbonyl group
  • Aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateLiquid
Charge0
Melting point-93 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility224 g/LALOGPS
logP-0.59ALOGPS
logP-0.13ChemAxon
logS0.48ALOGPS
pKa (Strongest Acidic)2.61ChemAxon
pKa (Strongest Basic)-9.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.37 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity13.5 m³·mol⁻¹ChemAxon
Polarizability5.35 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracelular
  • Peroxisome
Organoleptic PropertiesNot Available
SMPDB Pathways
Cysteine MetabolismPW002383 ThumbThumb?image type=greyscaleThumb?image type=simple
Ether lipid metabolismPW002492 ThumbThumb?image type=greyscaleThumb?image type=simple
Fatty acid biosynthesisPW002458 ThumbThumb?image type=greyscaleThumb?image type=simple
Glyoxylate cyclePW002419 ThumbThumb?image type=greyscaleThumb?image type=simple
Methionine metabolism and salvagePW002384 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Arginine and proline metabolismec00330 Map00330
Ether lipid metabolismec00565 Map00565
Fatty acid biosynthesisec00061 Map00061
Glycine, serine and threonine metabolismec00260 Map00260
Glyoxylate and dicarboxylate metabolismec00630 Map00630
SMPDB Reactions
Glyoxylic acid + L-AlaninePyruvic acid + Glycine
Glyoxylic acid + Acetyl-CoA + waterCoenzyme A + hydron + (S)-Malic acid
D-threo-Isocitric acidSuccinic acid + Glyoxylic acid
KEGG Reactions
Glyoxylic acid + L-AlaninePyruvic acid + Glycine
Isocitric acidGlyoxylic acid + Succinic acid
Glyoxylic acid + Acetyl-CoA + waterhydron + Coenzyme A + (S)-malate(2-)
water + hydron + Ureidoglycolic acidGlyoxylic acid + Carbon dioxide + Ammonium
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
  • 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
  • Kunze, M., Kragler, F., Binder, M., Hartig, A., Gurvitz, A. (2002). "Targeting of malate synthase 1 to the peroxisomes of Saccharomyces cerevisiae cells depends on growth on oleic acid medium." Eur J Biochem 269:915-922.11846793
  • Yoo, H. S., Cooper, T. G. (1991). "The ureidoglycollate hydrolase (DAL3) gene in Saccharomyces cerevisiae." Yeast 7:693-698.1776360
Synthesis Reference:Jie, Yuanping; Song, Zhen. Method for preparing glyoxylic acid. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 5pp.
External Links:
ResourceLink
CHEBI ID16891
HMDB IDHMDB00119
Pubchem Compound ID760
Kegg IDC00048
ChemSpider ID740
FOODB IDFDB001478
WikipediaGlyoxylic_acid
BioCyc IDGLYOX

Enzymes

General function:
Involved in metabolic process
Specific function:
Has alanine:glyoxylate aminotransferase activity
Gene Name:
AGX1
Uniprot ID:
P43567
Molecular weight:
41906.80078
Reactions
L-alanine + glyoxylate → pyruvate + glycine.
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 ureidoglycolate hydrolase activity
Specific function:
Utilization of purines as secondary nitrogen sources, when primary sources are limiting
Gene Name:
DAL3
Uniprot ID:
P32459
Molecular weight:
21726.59961
Reactions
(S)-ureidoglycolate + H(2)O → glyoxylate + 2 NH(3) + CO(2).
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 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
P53839
Molecular weight:
38831.19922
Reactions
glycolate + NADP+ → glyoxylate + NADPH + H+.