L-Idonate (PAMDB001772)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001772
Identification
Name: L-Idonate
Description:L-idonate is a member of the chemical class known as Sugar Acids and Derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group. L-idonate is a metabolite in D-gluconate catabolism. The catabolic sequence for l-idonate is as follows: l-idonate is transported by the l-idonate transporter, IdnT; l-idonate is oxidized to 5-keto-gluconate (5KG) by l-idonate 5-dehydrogenase, IdnD; 5KG is reduced to d-gluconate by 5-keto-D-gluconate 5-reductase, IdnO; and d-gluconate is phosphorylated by a thermosensitive gluconate kinase, IdnK, to make 6-phosphogluconate (6PG), which is further catabolized via the Entner-Doudoroff pathway. Thus, IdnD and IdnO allow for the redox-coupled interconversion of l-idonate to d-gluconate via 5KG. The l-idonate catabolic pathway overlaps d-gluconate catabolism through the common intermediates d-gluconate and 6PG.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • L-Idonate
  • L-Idonic acid
Chemical Formula: C6H12O7
Average Molecular Weight: 196.1553
Monoisotopic Molecular Weight: 196.058302738
InChI Key: RGHNJXZEOKUKBD-SKNVOMKLSA-N
InChI:InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3+,4-,5+/m0/s1
CAS number: 1114-17-6
IUPAC Name:(2R,3S,4R,5S)-2,3,4,5,6-pentahydroxyhexanoic acid
Traditional IUPAC Name: L-idonic acid
SMILES:[H][C@](O)(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]([H])(O)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as sugar acids and derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassSugar acids and derivatives
Direct Parent Sugar acids and derivatives
Alternative Parents
Substituents
  • Gluconic_acid
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Fatty acyl
  • Fatty acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Polyol
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Primary alcohol
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-1
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility159.0 mg/mLALOGPS
logP-2.6ALOGPS
logP-3.4ChemAxon
logS-0.09ALOGPS
pKa (Strongest Acidic)3.39ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area138.45 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity38.27 m3·mol-1ChemAxon
Polarizability17.02 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
L-Idonate + NADP <> 5-Dehydro-D-gluconate + NADPH + Hydrogen ion
NAD(P)<sup>+</sup> + L-Idonate <> NAD(P)H + 5-Keto-D-gluconate + Hydrogen ion
2-keto-L-gulonate + NAD(P)H + Hydrogen ion > L-Idonate + NAD(P)<sup>+</sup>
Hydrogen ion + 2-Dehydro-D-gluconate + NADPH <> L-Idonate + NADP
L-Idonate + NAD(P)(+) > 5-Keto-D-gluconate + NAD(P)H
L-Idonate + NAD + NADP <> 5-Keto-D-gluconate + NADH + NADPH + Hydrogen ion
Pathways: Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004j-2900000000-2230427d193bbdea286dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9500000000-d8d68bb3743d9921fc50View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0bvi-9100000000-ccfedd0f60a90274d462View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-05ic-9800000000-0ca5a02ddc6aa6467364View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052r-9400000000-eb28555aa63542892ef6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9100000000-ccfaef492473a4ca17deView in MoNA
References
References:
  • Bausch, C., Ramsey, M., Conway, T. (2004). "Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli." J Bacteriol 186:1388-1397. Pubmed: 14973046
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID17796
HMDB IDNot Available
Pubchem Compound ID604
Kegg IDC00770
ChemSpider ID584
Wikipedia IDNot Available
BioCyc IDL-IDONATE
EcoCyc IDL-IDONATE

Enzymes

Protein Details
• Glyoxylate/hydroxypyruvate reductase B
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. Can also reduce 2,5-diketo-D-gluconate (25DKG) to 5-keto-D- gluconate (5KDG), 2-keto-D-gluconate (2KDG) to D-gluconate, and 2- keto-L-gulonate (2KLG) to L-idonate (IA), but it is not its physiological function. Inactive towards 2-oxoglutarate, oxaloacetate, pyruvate, 5-keto-D-gluconate, D-fructose and L- sorbose. Activity with NAD is very low
Gene Name:
ghrB
Locus Tag:
PA2263
Molecular weight:
35.6 kDa
Reactions
Glycolate + NADP(+) = glyoxylate + NADPH.
D-glycerate + NAD(P)(+) = hydroxypyruvate + NAD(P)H.
D-gluconate + NADP(+) = 2-dehydro-D-gluconate + NADPH.

Transporters