ECMDB: 3-Deoxy-D-manno-octulosonate (ECMDB20069) (M2MDB000918)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (2)XML

Proteins (422)

Record Information

Version

2.0

Creation Date

2012-05-31 14:25:51 -0600

Update Date

2015-09-17 15:42:03 -0600

Secondary Accession Numbers

ECMDB20069

Identification

Name:

3-Deoxy-D-manno-octulosonate

Description

3-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

MOL SDF PDB SMILES InChI

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar 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 Framework

Aliphatic acyclic compounds

External Descriptors

3-deoxy-D-manno-octulosonic acid (CHEBI:32817 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	64.9 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-3	ChemAxon
logS	-0.57	ALOGPS
pKa (Strongest Acidic)	2.9	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	155.52 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	48.24 m³·mol⁻¹	ChemAxon
Polarizability	20.91 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:

Lipopolysaccharide biosynthesis	PW000831
lipopolysaccharide biosynthesis II	PW001905
lipopolysaccharide biosynthesis III	PW002059

KEGG Pathways:

Lipopolysaccharide biosynthesis ec00540
Metabolic pathways eco01100

EcoCyc Pathways:

CMP-KDO biosynthesis I PWY-1269
superpathway of lipopolysaccharide biosynthesis LPSSYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dr-2590000000-c8365537f240bd17c092	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03k9-9420000000-7c62b05f704b94da4ed3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-074m-9200000000-1f9f181dd8666e848b35	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002s-7920000000-37d0c8b357cc7b9ec55b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9400000000-35aeded87e6a52f7d9d0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06rf-9300000000-6953cb4ddc486610ea71	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-7950000000-446f15944c20db6ad35a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-9200000000-b31695a3aea736e88e0a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-e15cd12fb8544fac2178	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fl9-1960000000-51fe300eedf94aa4af65	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0uk9-9700000000-ffaef97a55c72fe661fc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00fu-9100000000-08188961ad90e14c8a7e	View 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

Links

External Links:

Resource	Link
CHEBI ID	32817
HMDB ID	HMDB0304125
Pubchem Compound ID	817
Kegg ID	C01187
ChemSpider ID	794
Wikipedia ID	Not Available
BioCyc ID	KDO
EcoCyc ID	KDO

Enzymes

Protein Details

1. 3-deoxy-manno-octulosonate cytidylyltransferase

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.

Protein Details

2. 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

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.

3-Deoxy-D-manno-octulosonate (ECMDB20069) (M2MDB000918)

Structure for #<Compound:0xaaca759c>

Enzymes

Reactions

Reactions