Record Information
Version2.0
Creation Date2012-05-31 14:55:18 -0600
Update Date2015-06-03 17:20:27 -0600
Secondary Accession Numbers
  • ECMDB21031
Identification
Name:KDO2-Lipid A
DescriptionKDO2-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
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
Weight:Average: 2238.7184
Monoisotopic: 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
ClassificationNot classified
Physical Properties
State:Not Available
Charge:-5
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.019 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count98ChemAxon
Refractivity564.64 m³·mol⁻¹ChemAxon
Polarizability249.16 ųChemAxon
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
Hydrogen ion + Palmitic acid + KDO2-Lipid A > Water + Hepta-acylated KDO2-lipid A
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
a phospholipid + KDO2-Lipid A > a glycerol ester + Hepta-acylated KDO2-lipid A
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
undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose + KDO2-Lipid A + 2 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
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Cationic antimicrobial peptide (CAMP) resistance eco01503
  • Lipopolysaccharide biosynthesis ec00540
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:Not Available
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

General function:
Involved in transferase activity, transferring acyl groups
Specific function:
Transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA. Decanoyl, palmitoyl, palmitoleoyl, and (R)-3-hydroxymyristoyl-ACP are poor acyl donors. Functions optimally after laurate incorporation by htrB has taken place. Acylates (KDO)2-(lauroyl)-lipid IVA about 100 times faster than (KDO)2-lipid IVA. Displays a preference for myristoyl-ACP over lauroyl-ACP
Gene Name:
msbB
Uniprot ID:
P24205
Molecular weight:
37410
General function:
Involved in catalytic activity
Specific function:
Catalyzes the addition of a phosphoethanolamine (pEtN) moiety to the outer 3-deoxy-D-manno-octulosonic acid (KDO) residue of a KDO(2)-lipid A. Phosphatidylethanolamines with one unsaturated acyl group functions as pEtN donors and the reaction releases diacylglycerol
Gene Name:
eptB
Uniprot ID:
P37661
Molecular weight:
63804
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
Uniprot ID:
P76473
Molecular weight:
62542
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.
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
Uniprot ID:
P24173
Molecular weight:
35544
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
Uniprot ID:
P0ADC6
Molecular weight:
39618
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
Uniprot ID:
P0AF98
Molecular weight:
40357
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
Uniprot ID:
P60752
Molecular weight:
64460
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
Uniprot ID:
P0A9V1
Molecular weight:
26800
General function:
Not Available
Specific function:
Not known; overproduction leads to camphor resistance and chromosome condensation
Gene Name:
crcA
Uniprot ID:
P37001
Molecular weight:
21770
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
Uniprot ID:
P0ADV9
Molecular weight:
21703
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
Uniprot ID:
P0ADV1
Molecular weight:
20127

Transporters

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
Uniprot ID:
P0ADC6
Molecular weight:
39618
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
Uniprot ID:
P0AF98
Molecular weight:
40357
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
Uniprot ID:
P60752
Molecular weight:
64460