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KDO-lipid IV(A) (M2MDB001644)

Record Information
Version2.0
Creation Date2012-07-30 14:55:04 -0600
Update Date2015-06-03 17:20:58 -0600
Secondary Accession Numbers
  • ECMDB21236
Identification
Name:KDO-lipid IV(A)
DescriptionKDO-lipid IV(a) is a part of lipopolysaccharide or LPS. Specifically it is lipid IVA glycosylated with a single 3-deoxy-D-manno-octulosonic acid (KDO) residue. KDO-lipid IV(a) is a saccharolipid. The most familiar saccharolipids are the acylated glucosamine precursors of the lipid A component of the lipopolysaccharides in Gram-negative bacteria. Typical lipid A molecules are disaccharides of glucosamine, which are derivatized with as many as seven fatty-acyl chains. The minimal lipopolysaccharide required for growth in E. coli is Kdo2-Lipid A, a hexa-acylated disaccharide of glucosamine that is glycosylated with two 3-deoxy-D-manno-octulosonic acid (Kdo) residues.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (KDO)-lipid IVA
  • (KDO)-lipid IVA
  • 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2->6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
  • 3-Deoxy-a-D-manno-oct-2-ulopyranosyl-(2->6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-b-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-a-D-glucopyranose
  • 3-Deoxy-alpha-D-manno-oct-2-ulopyranosyl-(2->6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose
  • 3-Deoxy-D-manno-octulosonyl-2',3',2',3'-tetrakis(b-hydroxymyristoyl)-D-glucosaminyl-1,6-b-D-glucosamine 1,4'-bisphosphate
  • 3-Deoxy-D-manno-octulosonyl-2',3',2',3'-tetrakis(b-hydroxymyristoyl)-D-glucosaminyl-1,6-b-D-glucosamine 1,4'-bisphosphoric acid
  • 3-Deoxy-D-manno-octulosonyl-2',3',2',3'-tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate
  • 3-Deoxy-D-manno-octulosonyl-2',3',2',3'-tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphoric acid
  • 3-Deoxy-D-manno-octulosonyl-2',3',2',3'-tetrakis(β-hydroxymyristoyl)-D-glucosaminyl-1,6-β-D-glucosamine 1,4'-bisphosphate
  • 3-Deoxy-D-manno-octulosonyl-2',3',2',3'-tetrakis(β-hydroxymyristoyl)-D-glucosaminyl-1,6-β-D-glucosamine 1,4'-bisphosphoric acid
  • 3-Deoxy-D-manno-octulosonyl-lipid IV(A)
  • 3-Deoxy-α-D-manno-oct-2-ulopyranosyl-(2->6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
  • KDO-lipid IV(A)
Chemical Formula:C76H142N2O30P2
Weight:Average: 1625.8836
Monoisotopic: 1624.912264238
InChI Key:GPNCBCJEDRRCDW-ACUQGRCXSA-N
InChI:InChI=1S/C76H142N2O30P2/c1-5-9-13-17-21-25-29-33-37-41-53(80)45-61(86)77-65-71(104-63(88)47-55(82)43-39-35-31-27-23-19-15-11-7-3)68(91)59(102-74(65)108-110(97,98)99)51-100-73-66(78-62(87)46-54(81)42-38-34-30-26-22-18-14-10-6-2)72(105-64(89)48-56(83)44-40-36-32-28-24-20-16-12-8-4)70(107-109(94,95)96)60(103-73)52-101-76(75(92)93)49-57(84)67(90)69(106-76)58(85)50-79/h53-60,65-74,79-85,90-91H,5-52H2,1-4H3,(H,77,86)(H,78,87)(H,92,93)(H2,94,95,96)(H2,97,98,99)/t53-,54-,55-,56-,57-,58-,59-,60-,65-,66-,67-,68-,69-,70-,71-,72-,73-,74-,76-/m1/s1
CAS number:Not Available
IUPAC Name:(2R,4R,5R,6R)-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxy-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)-lipid iva
SMILES:CCCCCCCCCCC[C@@H](O)CC(=O)N[C@H]1[C@@H](OP(O)(O)=O)O[C@H](CO[C@@H]2O[C@H](CO[C@@]3(C[C@@H](O)[C@@H](O)[C@H](O3)[C@H](O)CO)C(O)=O)[C@@H](OP(O)(O)=O)[C@H](OC(=O)C[C@H](O)CCCCCCCCCCC)[C@H]2NC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H](O)[C@@H]1OC(=O)C[C@H](O)CCCCCCCCCCC
Chemical Taxonomy
Description belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentAcylaminosugars
Alternative Parents
Substituents
  • Acylaminosugar
  • Saccharolipid
  • Hexose phosphate
  • Disaccharide phosphate
  • N-acyl-alpha-hexosamine
  • C-glucuronide
  • C-glycosyl compound
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Tricarboxylic acid or derivatives
  • Beta-hydroxy acid
  • Ketal
  • Fatty acid ester
  • Monoalkyl phosphate
  • Fatty acyl
  • Fatty amide
  • Alkyl phosphate
  • Hydroxy acid
  • N-acyl-amine
  • Pyran
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Carboxylic acid
  • Oxacycle
  • Acetal
  • Organopnictogen compound
  • Organic nitrogen compound
  • Organic oxide
  • Primary alcohol
  • Alcohol
  • Carbonyl group
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-5
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.04 g/LALOGPS
logP3.72ALOGPS
logP11.31ChemAxon
logS-4.6ALOGPS
pKa (Strongest Acidic)0.6ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count26ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area509.84 ŲChemAxon
Rotatable Bond Count67ChemAxon
Refractivity400.81 m³·mol⁻¹ChemAxon
Polarizability178.81 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
CMP-3-Deoxy-D-manno-octulosonate + 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate > Cytidine monophosphate + Hydrogen ion + KDO-lipid IV(A)
CMP-3-Deoxy-D-manno-octulosonate + KDO-lipid IV(A) > Cytidine monophosphate + Hydrogen ion + KDO(2)-lipid IV(A)
2,3,2'3'-Tetrakis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate + CMP-3-Deoxy-D-manno-octulosonate + 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate <> KDO-lipid IV(A) + Cytidine monophosphate
KDO-lipid IV(A) + CMP-3-Deoxy-D-manno-octulosonate <> Di[3-deoxy-D-manno-octulosonyl]-lipid IV(A) + Cytidine monophosphate
CMP-3-Deoxy-D-manno-octulosonate + lipid IV<sub>A</sub> <> Hydrogen ion + KDO-lipid IV(A) + Cytidine monophosphate
KDO-lipid IV(A) + CMP-3-Deoxy-D-manno-octulosonate <> Hydrogen ion + &alpha;-Kdo-(2->4)-&alpha;-Kdo-(2->6)-lipid IV<SUB>A</SUB> + Cytidine monophosphate
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Lipopolysaccharide biosynthesis ec00540
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4r-0018189000-bab8c94d64d4d246a561View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004r-1519223000-af65ac0fd99c577268afView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0bw9-2329251000-b437d8f531d53e26bafbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-05p2-9163224001-ccfaf88f2e0f5454f666View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9110000000-7fa42647ff5cc1e51040View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-3eb605d4860dc7fbec9cView in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
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 ID27439
HMDB IDNot Available
Pubchem Compound ID819
Kegg IDC06024
ChemSpider ID26333135
Wikipedia IDNot Available
BioCyc IDKDO-LIPID-IVA
EcoCyc IDKDO-LIPID-IVA

Enzymes

Protein Details
1. 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
Uniprot ID:
P0AC75
Molecular weight:
47291