KDO2-Lipid A (PAMDB001447)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001447
Identification
Name: KDO2-Lipid A
Description:KDO2-Lipid A is an intermediate in the synthesis of LPS. It has two 3-deoxy-D-manno-octulosonic acid (KDO) sugar residues in place of the core, and has no O-antigen.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A
  • a-kdo-(2->4)-a-kdo-(2->6)-lipid a
  • Alpha-KDO-(2->4)-alpha-KDO-(2->6)-lipid A
  • Re endotoxin
  • α-kdo-(2->4)-α-kdo-(2->6)-lipid a
Chemical Formula: C110H202N2O39P2
Average Molecular Weight: 2238.7184
Monoisotopic Molecular Weight: 2237.335997756
InChI Key: DIXUKJUHGLIZGU-ZKUMOPDFSA-N
InChI:InChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/t79?,80?,81?,82?,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1
CAS number: Not Available
IUPAC Name:(2R,4R,5R,6R)-4-{[(2R,4R,5R,6R)-2-carboxy-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-[(1,3-dihydroxytetradecylidene)amino]-3-hydroxy-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxane-2-carboxylic acid
Traditional IUPAC Name: (2R,4R,5R,6R)-4-{[(2R,4R,5R,6R)-2-carboxy-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-[(1,3-dihydroxytetradecylidene)amino]-3-hydroxy-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxane-2-carboxylic acid
SMILES:[H]C(O)(CCCCCCCCCCC)CC(=O)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO[C@]2([H])O[C@]([H])(CO[C@@]3(C[C@@]([H])(O[C@@]4(C[C@@]([H])(O)[C@@]([H])(O)[C@]([H])(O4)[C@]([H])(O)CO)C(O)=O)[C@@]([H])(O)[C@]([H])(O3)[C@]([H])(O)CO)C(O)=O)[C@@]([H])(OP(O)(O)=O)[C@]([H])(OC(=O)CC([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C(O)CC([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C(O)CC([H])(O)CCCCCCCCCCC
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as hexacarboxylic acids and derivatives. These are carboxylic acids containing exactly six carboxyl groups.
Kingdom Organic compounds
Super ClassOrganic acids and derivatives
Class Carboxylic acids and derivatives
Sub ClassHexacarboxylic acids and derivatives
Direct Parent Hexacarboxylic acids and derivatives
Alternative Parents
Substituents
  • Hexacarboxylic acid or derivatives
  • Saccharolipid
  • N-acyl-alpha-hexosamine
  • Disaccharide phosphate
  • C-glucuronide
  • Glucosamine
  • Amino sugar
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • C-glycosyl compound
  • Pyran carboxylic acid
  • Pyran carboxylic acid or derivatives
  • Monoalkyl phosphate
  • Amino saccharide
  • Fatty acid ester
  • Beta-hydroxy acid
  • Fatty acyl
  • Alkyl phosphate
  • Pyran
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydroxy acid
  • Secondary alcohol
  • Carboxylic acid ester
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid
  • Carboximidic acid derivative
  • Carboximidic acid
  • Acetal
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-5
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.0186 mg/mLALOGPS
logP4.35ALOGPS
logP22.64ChemAxon
logS-5.1ALOGPS
pKa (Strongest Acidic)0.55ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count35ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area645.41 Å2ChemAxon
Rotatable Bond Count98ChemAxon
Refractivity564.64 m3·mol-1ChemAxon
Polarizability249.16 Å3ChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
Adenosine triphosphate + Water + KDO2-Lipid A > ADP + Hydrogen ion + Phosphate + KDO2-Lipid A
Adenosine triphosphate + Water + KDO2-Lipid A > ADP + Hydrogen ion + Phosphate + KDO2-Lipid A
-->-->KDO(2)-lipid IV(A) with laurate + Myristoyl-ACP (n-C14:0ACP) > acyl carrier protein + KDO2-Lipid A
KDO2-Lipid A + PE(14:0/14:0) > 1,2-Diacyl-sn-glycerol (dihexadec-9-enoyl, n-C16:1) + Phosphoethanolamine KDO(2)-lipid (A)
KDO2-Lipid A + PE(14:0/14:0) > 1,2-Diacyl-sn-glycerol (dioctadec-11-enoyl, n-C18:1) + Phosphoethanolamine KDO(2)-lipid (A)
ADP-L-Glycero-D-manno-heptose + KDO2-Lipid A > ADP + Hydrogen ion + heptosyl-kdo2-lipidA
KDO2-Lipid A + Acyl-carrier protein + Tetradecanoyl-[acp] + Lauroyl-KDO2-lipid IV(A) <> Tetradecanoyl-[acp] + Lauroyl-KDO2-lipid IV(A) + Acyl-carrier protein
KDO2-Lipid A + 4-amino-4-deoxy-&alpha;-L-arabinopyranosyl <i>ditrans,octacis</i>-undecaprenyl phosphate > L-Ara4N-modified KDO2-Lipid A + Di-trans,poly-cis-undecaprenyl phosphate
Hydrogen ion + KDO2-Lipid A + ADP-L-Glycero-D-manno-heptose > Heptosyl-KDO2-lipid A + ADP
undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose + KDO2-Lipid A + 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate <> alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-[4-P-L-Ara4N]-lipid A + Di-trans,poly-cis-undecaprenyl phosphate + Lipid IIA
Pathways:
  • Cationic antimicrobial peptide (CAMP) resistance pae01503
  • Lipopolysaccharide biosynthesis pae00540
Spectra
Spectra:
References
References:
  • 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
  • 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 ID27963
HMDB IDNot Available
Pubchem Compound ID440886
Kegg IDC06026
ChemSpider ID389718
Wikipedia IDNot Available
BioCyc IDKDO2-LIPID-A
EcoCyc IDKDO2-LIPID-A

Enzymes

Protein Details
• Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnT
Locus Tag:
PA3556
Molecular weight:
61.7 kDa
Reactions
4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + lipid IV(A) = lipid II(A) + di-trans,octa-cis-undecaprenyl phosphate.
Protein Details
• Lipopolysaccharide heptosyltransferase 1
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
Heptose transfer to the lipopolysaccharide core. It transfers the innnermost heptose to [4'-P](3-deoxy-D-manno- octulosonic acid)2-IVA
Gene Name:
rfaC
Locus Tag:
PA5011
Molecular weight:
39.7 kDa
Protein Details
• Lipopolysaccharide export system permease protein lptG
General function:
Involved in lipopolysaccharide transport
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptG
Locus Tag:
PA3827
Molecular weight:
39.2 kDa
Protein Details
• Lipopolysaccharide export system permease protein lptF
General function:
Involved in lipopolysaccharide-transporting ATPase acti
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptF
Locus Tag:
PA3828
Molecular weight:
41.3 kDa
Protein Details
• Lipid A export ATP-binding/permease protein msbA
General function:
Involved in nucleotide binding
Specific function:
Involved in lipid A export and possibly also in glycerophospholipid export and for biogenesis of the outer membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation
Gene Name:
msbA
Locus Tag:
PA4997
Molecular weight:
66.4 kDa
Protein Details
• Lipopolysaccharide export system ATP-binding protein lptB
General function:
Involved in nucleotide binding
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane. Probably responsible for energy coupling to the transport system
Gene Name:
lptB
Locus Tag:
PA4461
Molecular weight:
26.5 kDa
Protein Details
• Lipopolysaccharide export system protein lptC
General function:
Involved in lipopolysaccharide transmembrane transporter activity
Specific function:
Required for the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptC
Locus Tag:
PA4459
Molecular weight:
21.4 kDa
Protein Details
• Lipopolysaccharide export system protein lptA
General function:
Involved in lipopolysaccharide binding
Specific function:
Required for the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane. May act as a chaperone that facilitates LPS transfer across the aquaeous environment of the periplasm. Interacts specifically with the lipid A domain of LPS
Gene Name:
lptA
Locus Tag:
PA0005
Molecular weight:
28.7 kDa

Transporters

Protein Details
• Lipopolysaccharide export system permease protein lptG
General function:
Involved in lipopolysaccharide transport
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptG
Locus Tag:
PA3827
Molecular weight:
39.2 kDa
Protein Details
• Lipopolysaccharide export system permease protein lptF
General function:
Involved in lipopolysaccharide-transporting ATPase acti
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptF
Locus Tag:
PA3828
Molecular weight:
41.3 kDa
Protein Details
• Lipid A export ATP-binding/permease protein msbA
General function:
Involved in nucleotide binding
Specific function:
Involved in lipid A export and possibly also in glycerophospholipid export and for biogenesis of the outer membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation
Gene Name:
msbA
Locus Tag:
PA4997
Molecular weight:
66.4 kDa