ECMDB: 2-Keto-3-deoxy-D-gluconic acid (ECMDB01353) (M2MDB000352)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (6)Transporters (7)XML

Proteins (713)

Record Information

Version

2.0

Creation Date

2012-05-31 13:50:40 -0600

Update Date

2015-09-17 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

MOL SDF PDB SMILES InChI

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

Description

belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Medium-chain keto acids and derivatives

Direct Parent

Medium-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 Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid (CHEBI:17032 )
hexonic acid (CHEBI:17032 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source
LogP:	-2.175	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	134 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-1.8	ChemAxon
logS	-0.12	ALOGPS
pKa (Strongest Acidic)	2.91	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	36.32 m³·mol⁻¹	ChemAxon
Polarizability	15.52 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

hexuronide and hexuronate degradation	PW000834
inner membrane transport	PW000786

KEGG Pathways:

Metabolic pathways eco01100
Microbial metabolism in diverse environments ec01120
Pentose and glucuronate interconversions ec00040
Pentose phosphate pathway ec00030

EcoCyc Pathways:

β-D-glucuronide and D-glucuronate degradation GLUCUROCAT-PWY
D-galacturonate degradation I GALACTUROCAT-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03fu-1900000000-b83e7928054ed87e61ea	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p6-7900000000-0ec05107fe4cacbafdc2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dv-9200000000-1155f7c7fe0875a6e135	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-ac6a432df8fcf15017f9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9400000000-ad5a44111e40a3f47da6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-059f-9200000000-b4281968f243d4a223b5	View 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

Links

External Links:

Resource	Link
CHEBI ID	17032
HMDB ID	HMDB01353
Pubchem Compound ID	161227
Kegg ID	C00204
ChemSpider ID	141630
Wikipedia ID	Not Available
BioCyc ID	2-DEHYDRO-3-DEOXY-D-GLUCONATE
EcoCyc ID	2-DEHYDRO-3-DEOXY-D-GLUCONATE
Ligand Expo	KDG

Enzymes

Protein Details

1. 2-keto-3-deoxygluconate permease

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

Protein Details

2. Mannonate dehydratase

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.

Protein Details

3. 2-dehydro-3-deoxygluconokinase

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.

Protein Details

4. 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase

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.

Protein Details

5. Altronate hydrolase

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.

Protein Details

6. Starvation-sensing protein RspA

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

Protein Details

1. 2-keto-3-deoxygluconate permease

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

Protein Details

2. 2-keto-3-deoxygluconate permease

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

Protein Details

3. 2-keto-3-deoxygluconate permease

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

Protein Details

4. Outer membrane protein N

General function:: Involved in transporter activity
Specific function:: Non-specific porin
Gene Name:: ompN
Uniprot ID:: P77747
Molecular weight:: 41220

Protein Details

5. Outer membrane pore protein E

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

Protein Details

6. Outer membrane protein F

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

Protein Details

7. Outer membrane protein C

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

2-Keto-3-deoxy-D-gluconic acid (ECMDB01353) (M2MDB000352)

Structure for #<Compound:0xaa15390c>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Transporters