Record Information
Version2.0
Creation Date2012-05-31 14:25:51 -0600
Update Date2015-09-17 15:42:03 -0600
Secondary Accession Numbers
  • ECMDB20069
Identification
Name:3-Deoxy-D-manno-octulosonate
Description3-deoxy-D-manno-octulosonate is a member of the chemical class known as Octoses. These are monosaccahride compounds in which the sugar moiety is an octose (8 carbon atoms). 3-Deoxy-D-manno-octulosonic acid (KDO) is an eight-carbon sugar ubiquitous in Gram-negative bacterial lipopolysaccharides (LPS). (PMID 20801884) The enzyme 3-deoxy-D-manno-octulosonic acid (KDO) transferase is encoded by the kdtA gene of Escherichia coli and plays a key role in lipopolysaccharide biosynthesis.(PMID 1577828) KDO is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. (PMID 19726684) KDO8P is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the lipopolysaccharide of Gram-negative bacteria. (PMID 10734095)
Structure
Thumb
Synonyms:
  • 2-Dehydro-3-deoxy-D-octonate
  • 2-Dehydro-3-deoxy-D-octonic acid
  • 2-Keto-3-deoxy-D-manno-octonate
  • 2-Keto-3-deoxy-D-manno-octonic acid
  • 2-Keto-3-deoxyoctonate
  • 2-Keto-3-deoxyoctonic acid
  • 2-Keto-3-deoxyoctulosonate
  • 2-Keto-3-deoxyoctulosonic acid
  • 3-Deoxy-2-Octulosonate
  • 3-Deoxy-2-Octulosonic acid
  • 3-Deoxy-a-D-manno-2-octulosonate
  • 3-Deoxy-a-D-manno-2-octulosonic acid
  • 3-Deoxy-alpha-D-manno-2-octulosonate
  • 3-Deoxy-alpha-D-manno-2-octulosonic acid
  • 3-Deoxy-D-manno-2-octulosonate
  • 3-Deoxy-D-manno-2-octulosonic acid
  • 3-deoxy-D-manno-octulosonate
  • 3-Deoxy-D-manno-octulosonic acid
  • 3-Deoxy-D-mannoctulosonate
  • 3-Deoxy-D-mannoctulosonic acid
  • 3-Deoxy-D-mannooctulosonate
  • 3-Deoxy-D-mannooctulosonic acid
  • 3-Deoxy-α-D-manno-2-octulosonate
  • 3-Deoxy-α-D-manno-2-octulosonic acid
  • 3-Deoxyoctulosonate
  • 3-Deoxyoctulosonic acid
  • 3-KDO
  • Deoxy-manno-octulosonate
  • Deoxy-manno-octulosonic acid
  • DManOA
  • KDO
  • Ketodeoxyoctonate
  • Ketodeoxyoctonic acid
Chemical Formula:C8H13O8
Weight:Average: 237.185
Monoisotopic: 237.061590959
InChI Key:KYQCXUMVJGMDNG-UHFFFAOYSA-M
InChI:InChI=1S/C8H14O8/c9-2-5(12)7(14)6(13)3(10)1-4(11)8(15)16/h3,5-7,9-10,12-14H,1-2H2,(H,15,16)/p-1
CAS number:1069-03-0
IUPAC Name:(4R,5R,6R,7R)-4,5,6,7,8-pentahydroxy-2-oxooctanoic acid
Traditional IUPAC Name:3-deoxy-D-manno-octulosonate
SMILES:OCC(O)C(O)C(O)C(O)CC(=O)C([O-])=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Octose monosaccharide
  • Medium-chain keto acid
  • Sugar acid
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • Monosaccharide
  • Keto acid
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Alcohol
  • Carbonyl group
  • Primary 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
Predicted Properties
PropertyValueSource
Water Solubility64.9 g/LALOGPS
logP-2.5ALOGPS
logP-3ChemAxon
logS-0.57ALOGPS
pKa (Strongest Acidic)2.9ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area155.52 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity48.24 m³·mol⁻¹ChemAxon
Polarizability20.91 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIPW001905 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIIPW002059 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00dr-2590000000-c8365537f240bd17c092View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03k9-9420000000-7c62b05f704b94da4ed3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-074m-9200000000-1f9f181dd8666e848b35View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002s-7920000000-37d0c8b357cc7b9ec55bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-9400000000-35aeded87e6a52f7d9d0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06rf-9300000000-6953cb4ddc486610ea71View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-7950000000-446f15944c20db6ad35aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-9200000000-b31695a3aea736e88e0aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-e15cd12fb8544fac2178View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fl9-1960000000-51fe300eedf94aa4af65View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0uk9-9700000000-ffaef97a55c72fe661fcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00fu-9100000000-08188961ad90e14c8a7eView in MoNA
References
References:
  • Belunis, C. J., Raetz, C. R. (1992). "Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli." J Biol Chem 267:9988-9997. Pubmed: 1577828
  • Biswas, T., Yi, L., Aggarwal, P., Wu, J., Rubin, J. R., Stuckey, J. A., Woodard, R. W., Tsodikov, O. V. (2009). "The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase." J Biol Chem 284:30594-30603. Pubmed: 19726684
  • Chalabaev, S., Kim, T. H., Ross, R., Derian, A., Kasper, D. L. (2010). "3-Deoxy-D-manno-octulosonic acid (Kdo) hydrolase identified in Francisella tularensis, Helicobacter pylori, and Legionella pneumophila." J Biol Chem 285:34330-34336. Pubmed: 20801884
  • 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
  • Radaev, S., Dastidar, P., Patel, M., Woodard, R. W., Gatti, D. L. (2000). "Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase." J Biol Chem 275:9476-9484. Pubmed: 10734095
  • 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
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID32817
HMDB IDHMDB0304125
Pubchem Compound ID817
Kegg IDC01187
ChemSpider ID794
Wikipedia IDNot Available
BioCyc IDKDO
EcoCyc IDKDO

Enzymes

General function:
Involved in lipopolysaccharide biosynthetic process
Specific function:
Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria
Gene Name:
kdsB
Uniprot ID:
P04951
Molecular weight:
27614
Reactions
CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.
General function:
Involved in 3-deoxy-manno-octulosonate-8-phosphatase activity
Specific function:
Catalyzes the hydrolysis of KDO 8-P to KDO and inorganic phosphate
Gene Name:
kdsC
Uniprot ID:
P0ABZ4
Molecular weight:
19997
Reactions
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate.