Record Information
Version2.0
Creation Date2012-05-31 13:50:40 -0600
Update Date2015-09-17 19:21:29 -0600
Secondary Accession Numbers
  • ECMDB01353
Identification
Name:2-Keto-3-deoxy-D-gluconic acid
Description:2-keto-3-deoxy-D-gluconic acid is a member of the chemical class known as Hexoses. These are monosaccharides in which the sugar unit is a hexose. KDG, an actual inducer of pectinolysis, releases the repressor from the operator complexes, whereas galacturonate, which is the precursor of the actual inducer, does not. (PMID 1545709) KDG aldolase, KDGA, is a homotetramer of 32-kDa subunits. (PMID 20023024) The KDG-aldolase is a thermostable tetrameric protein with a half-life at 100 degrees C of 2. (PMID 10527934)
Structure
Thumb
Synonyms:
  • 2-Dehydro-3-deoxy-D-gluconate
  • 2-Dehydro-3-deoxy-D-gluconic acid
  • 2-Keto-3-deoxy-D-gluconate
  • 2-Keto-3-deoxy-D-gluconic acid
  • 2-Keto-3-deoxygluconate
  • 2-Keto-3-deoxygluconic acid
  • 3-Deoxy-2-oxo-D-gluconate
  • 3-Deoxy-2-oxo-D-gluconic acid
  • 3-deoxy-D-erythro-hex-2-ulosonic acid
  • 3-Deoxy-D-erythro-2-hexulosonate
  • 3-Deoxy-D-erythro-2-hexulosonic acid
  • 3-Deoxy-D-erythro-hex-2-ulosonate
  • 3-Deoxy-D-erythro-hex-2-ulosonic acid
  • KDG
Chemical Formula:C6H10O6
Weight:Average: 178.14
Monoisotopic: 178.047738052
InChI Key:WPAMZTWLKIDIOP-NQXXGFSBSA-N
InChI:InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1
CAS number:17510-99-5
IUPAC Name:(4S,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
Traditional IUPAC Name:2-dehydro-3-deoxy-D-gluconate
SMILES:OC[C@@H](O)[C@H](O)CC(=O)C(O)=O
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic acids and derivatives
Sub ClassKeto acids and derivatives
Direct ParentMedium-chain keto acids and derivatives
Alternative Parents
Substituents
  • Medium-chain keto acid
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Primary alcohol
  • Organooxygen compound
  • Organic oxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
LogP:-2.175PhysProp
Predicted Properties
PropertyValueSource
Water Solubility134.0 mg/mLALOGPS
logP-1.9ALOGPS
logP-1.8ChemAxon
logS-0.12ALOGPS
pKa (Strongest Acidic)2.91ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115.06 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.32 m3·mol-1ChemAxon
Polarizability15.52 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
hexuronide and hexuronate degradationPW000834 Pw000834Pw000834 greyscalePw000834 simple
inner membrane transportPW000786 Pw000786Pw000786 greyscalePw000786 simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03fu-1900000000-b83e7928054ed87e61eaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01p6-7900000000-0ec05107fe4cacbafdc2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00dv-9200000000-1155f7c7fe0875a6e135View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-3900000000-ac6a432df8fcf15017f9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-9400000000-ad5a44111e40a3f47da6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-059f-9200000000-b4281968f243d4a223b5View in MoNA
References
References:
  • Buchanan, C. L., Connaris, H., Danson, M. J., Reeve, C. D., Hough, D. W. (1999). "An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates." Biochem J 343 Pt 3:563-570. Pubmed: 10527934
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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
  • Nasser, W., Reverchon, S., Robert-Baudouy, J. (1992). "Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi." Mol Microbiol 6:257-265. Pubmed: 1545709
  • Reher, M., Fuhrer, T., Bott, M., Schonheit, P. (2010). "The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase." J Bacteriol 192:964-974. Pubmed: 20023024
  • 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 ID17032
HMDB IDHMDB01353
Pubchem Compound ID161227
Kegg IDC00204
ChemSpider ID141630
Wikipedia IDNot Available
BioCyc ID2-DEHYDRO-3-DEOXY-D-GLUCONATE
EcoCyc ID2-DEHYDRO-3-DEOXY-D-GLUCONATE
Ligand ExpoKDG

Enzymes

General function:
Involved in 2-keto-3-deoxygluconate:hydrogen symporter activity
Specific function:
The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system
Gene Name:
kdgT
Uniprot ID:
P0A712
Molecular weight:
33669
General function:
Involved in mannonate dehydratase activity
Specific function:
D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H(2)O
Gene Name:
uxuA
Uniprot ID:
P24215
Molecular weight:
44838
Reactions
D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H(2)O.
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 6- phospho-2-dehydro-3-deoxy-D-gluconate
Gene Name:
kdgK
Uniprot ID:
P37647
Molecular weight:
33962
Reactions
ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 6-phospho-2-dehydro-3-deoxy-D-gluconate.
General function:
Involved in 2-deoxy-D-gluconate 3-dehydrogenase activity
Specific function:
Catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3- deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH
Gene Name:
kduD
Uniprot ID:
P37769
Molecular weight:
27070
Reactions
2-dehydro-3-deoxy-D-gluconate + NAD(+) = (4S)-4,6-dihydroxy-2,5-dioxohexanoate + NADH.
General function:
Involved in hydro-lyase activity
Specific function:
D-altronate = 2-dehydro-3-deoxy-D-gluconate + H(2)O
Gene Name:
uxaA
Uniprot ID:
P42604
Molecular weight:
54093
Reactions
D-altronate = 2-dehydro-3-deoxy-D-gluconate + H(2)O.
General function:
cellular amino acid catabolic process
Specific function:
Probably involved in the degradation of homoserine lactone (HSL) or of a metabolite of HSL that signals starvation.
Gene Name:
rspA
Uniprot ID:
P38104
Molecular weight:
45968
Reactions
=

Transporters

General function:
Involved in 2-keto-3-deoxygluconate:hydrogen symporter activity
Specific function:
The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system
Gene Name:
kdgT
Uniprot ID:
P0A712
Molecular weight:
33669
General function:
Involved in 2-keto-3-deoxygluconate:hydrogen symporter activity
Specific function:
The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system
Gene Name:
kdgT
Uniprot ID:
B1XB76
Molecular weight:
33669
General function:
Involved in 2-keto-3-deoxygluconate:hydrogen symporter activity
Specific function:
The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system
Gene Name:
kdgT
Uniprot ID:
C5A077
Molecular weight:
33669
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368