KDO(2)-lipid IV(A) (PAMDB001643)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001643
Identification
Name: KDO(2)-lipid IV(A)
Description:Kdo(2)-lipid iv(a) belongs to the class of Polysaccharide Phosphates. These are polysaccharides in which a phosphate group is bound to at least one carbohydrate unit. (inferred from compound structure)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • (2R,4R,5R,6R)-2-(2R,4R,5R,6R)-2-Carboxy-6-(1R)-1,2-dihydroxyethyl-5-hydroxy-2-(2R,3S,4R,5R,6R)-6-(2R,3S,4R,5R,6R)-3-hydroxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-6-phosphonooxyoxan-2-ylmethoxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-3-phosphonooxyoxan-2-ylmethoxyoxan-4-yloxy-6-(1R)-1,2-dihydroxyethyl-4,5-dihydroxyoxane-2-carboxylate
  • (2R,4R,5R,6R)-2-(2R,4R,5R,6R)-2-carboxy-6-(1R)-1,2-dihydroxyethyl-5-hydroxy-2-(2R,3S,4R,5R,6R)-6-(2R,3S,4R,5R,6R)-3-hydroxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-6-phosphonooxyoxan-2-ylmethoxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-3-phosphonooxyoxan-2-ylmethoxyoxan-4-yloxy-6-(1R)-1,2-dihydroxyethyl-4,5-dihydroxyoxane-2-carboxylic acid
  • (2R,4R,5R,6R)-4-(2R,4R,5R,6R)-2-Carboxy-6-(1R)-1,2-dihydroxyethyl-4,5-dihydroxy-tetrahydropyran-2-yloxy-6-(1R)-1,2-dihydroxyethyl-5-hydroxy-2-(2R,3S,4R,5R,6R)-6-(2R,3S,4R,5R,6R)-3-hydroxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-6-phosphonooxy-tetrahydropyran-2-ylmethoxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-3-phosphonooxy-tetrahydropyran-2-ylmethoxytetrahydropyran-2-carboxylate
  • (2R,4R,5R,6R)-4-(2R,4R,5R,6R)-2-carboxy-6-(1R)-1,2-dihydroxyethyl-4,5-dihydroxy-tetrahydropyran-2-yloxy-6-(1R)-1,2-dihydroxyethyl-5-hydroxy-2-(2R,3S,4R,5R,6R)-6-(2R,3S,4R,5R,6R)-3-hydroxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-6-phosphonooxy-tetrahydropyran-2-ylmethoxy-5-(3R)-3-hydroxytetradecanoylamino-4-(3R)-3-hydroxytetradecanoyloxy-3-phosphonooxy-tetrahydropyran-2-ylmethoxytetrahydropyran-2-carboxylic acid
  • Di3-deoxy-D-manno-octulosonyl-lipid IV(A)
  • KDO2-lipid IV(A)
Chemical Formula: C84H154N2O37P2
Average Molecular Weight: 1846.0603
Monoisotopic Molecular Weight: 1844.970566976
InChI Key: XAOLJGCZESYRFT-VHSKNIDJSA-N
InChI:InChI=1S/C84H154N2O37P2/c1-5-9-13-17-21-25-29-33-37-41-55(89)45-65(96)85-69-77(117-67(98)47-57(91)43-39-35-31-27-23-19-15-11-7-3)73(102)63(115-80(69)123-125(110,111)112)53-113-79-70(86-66(97)46-56(90)42-38-34-30-26-22-18-14-10-6-2)78(118-68(99)48-58(92)44-40-36-32-28-24-20-16-12-8-4)76(122-124(107,108)109)64(116-79)54-114-83(81(103)104)50-62(72(101)75(120-83)61(95)52-88)119-84(82(105)106)49-59(93)71(100)74(121-84)60(94)51-87/h55-64,69-80,87-95,100-102H,5-54H2,1-4H3,(H,85,96)(H,86,97)(H,103,104)(H,105,106)(H2,107,108,109)(H2,110,111,112)/t55-,56-,57-,58-,59-,60-,61-,62-,63-,64-,69-,70-,71-,72-,73-,74-,75-,76-,77-,78-,79-,80-,83-,84-/m1/s1
CAS number: 143600-83-3
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]-5-hydroxy-2-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-[(3R)-3-hydroxytetradecanamido]-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-5-[(3R)-3-hydroxytetradecanamido]-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-3-(phosphonooxy)oxan-2-yl]methoxy}oxane-2-carboxylic acid
Traditional IUPAC Name: (kdo)2-lipid iva
SMILES:[H]OC(=O)[C@]1(OC([H])([H])[C@@]2([H])O[C@@]([H])(OC([H])([H])[C@@]3([H])O[C@]([H])(OP(=O)(O[H])O[H])[C@]([H])(N([H])C(=O)C([H])([H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@@]([H])(OC(=O)C([H])([H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@]3([H])O[H])[C@]([H])(N([H])C(=O)C([H])([H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@@]([H])(OC(=O)C([H])([H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@]2([H])OP(=O)(O[H])O[H])O[C@]([H])([C@]([H])(O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@]([H])(O[C@]2(O[C@]([H])([C@]([H])(O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@]([H])(O[H])C2([H])[H])C(=O)O[H])C1([H])[H]
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as saccharolipids. These are compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a sugar substitutes for the glycerol backbone that is present in glycerolipids and glycerophospholipids. The most familiar saccharolipids contain an acylated glucosamine. In contrast to others glycolipids, the fatty acid is not glycosidically linked to the sugar moiety.
Kingdom Organic compounds
Super ClassLipids and lipid-like molecules
Class Saccharolipids
Sub ClassNot Available
Direct Parent Saccharolipids
Alternative Parents
Substituents
  • Saccharolipid
  • N-acyl-alpha-hexosamine
  • Disaccharide phosphate
  • C-glucuronide
  • Tetracarboxylic acid or derivatives
  • 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
  • Saccharide
  • 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
  • Carboxylic acid derivative
  • 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:-6
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
logP9.83ChemAxon
pKa (Strongest Acidic)0.6ChemAxon
Physiological Charge-6ChemAxon
Hydrogen Acceptor Count33ChemAxon
Hydrogen Donor Count20ChemAxon
Polar Surface Area626.29 Å2ChemAxon
Rotatable Bond Count72ChemAxon
Refractivity444.02 m3·mol-1ChemAxon
Polarizability195.55 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 + KDO(2)-lipid IV(A) > ADP + Hydrogen ion + Phosphate + KDO(2)-lipid IV(A)
Adenosine triphosphate + Water + KDO(2)-lipid IV(A) > ADP + Hydrogen ion + Phosphate + KDO(2)-lipid IV(A)
-->-->Dodecanoyl-ACP (n-C12:0ACP) + KDO(2)-lipid IV(A) > acyl carrier protein + KDO(2)-lipid IV(A) with laurate
cis-hexadec-9-enoyl-[acyl-carrier protein] (n-C16:1) + KDO(2)-lipid IV(A) > acyl carrier protein + KDO(2)-lipid IV(A) with palmitoleoyl
CMP-3-Deoxy-D-manno-octulosonate + KDO-lipid IV(A) > Cytidine monophosphate + Hydrogen ion + KDO(2)-lipid IV(A)
Lauroyl-KDO2-lipid IV(A) + Acyl-carrier protein + Dodecanoyl-[acyl-carrier protein] + KDO(2)-lipid IV(A) <> Dodecanoyl-[acyl-carrier protein] + Di[3-deoxy-D-manno-octulosonyl]-lipid IV(A) + Lauroyl-KDO2-lipid IV(A) + Acyl-carrier protein
Hexadecenoyl-[acyl-carrier protein] + KDO(2)-lipid IV(A) <> (9Z)-Hexadec-9-enoyl-KDO2-lipid IV(A) + Acyl-carrier protein
Pathways:
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
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID28526
HMDB IDNot Available
Pubchem Compound ID3083382
Kegg IDC06025
ChemSpider ID2340609
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
• 3-deoxy-D-manno-octulosonic-acid transferase
General function:
Involved in biosynthetic process
Specific function:
Essential step in lipopolysaccharides biosynthesis. Acts at transfer of 3-deoxy-D-mono octulonic acid (KDO) from CMP-KDO to a tetraacyldisaccharide 1,4'-bisphosphate precursor of lipid A (lipid IVA). Transfers two molecules of KDO to lipid IVA. Degraded by FtsH; therefore FtsH regulates the addition of the sugar moiety of the LPS and thus the maturation of the LPS precursor
Gene Name:
waaA
Locus Tag:
PA4988
Molecular weight:
46.5 kDa
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 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