Glucosyl-heptosyl3-KDO2-lipid A-bisphosphate (ECMDB20531) (M2MDB001339)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-05-31 14:49:18 -0600
Update Date2015-06-03 17:20:10 -0600
Secondary Accession Numbers
  • ECMDB20531
Identification
Name:Glucosyl-heptosyl3-KDO2-lipid A-bisphosphate
DescriptionGlucosyl-heptosyl3-kdo2-lipid a-bisphosphate is a component of LPS. Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain inserted into the outer membrane known as lipid A (or endotoxin), a phosphorylated "core" oligosaccharide and a distal polysaccharide (or O antigen). The core oligosaccharides are conceptually divided into two regions: inner core and outer core. The inner core is highly conserved, comprises three deoxy-D-manno-octulosonic acid (KDO) and L-glycero-D-manno-heptose (Hep) and is often phosphorylated. The inner core oligosaccharide plays a critical role in essential barrier function of the outer membrane. The outer core comprises a tri-hexose backbone modified with varying side-branch substitutions of hexose and acetamidohexose residues. The outer core provides an attachment site for O-antigen. The completed lipid A-KDO2 serves as the acceptor on which the core oligosaccharide chains are assembled by sequential glycosyl transfer from nucleotide sugar precursors. This process involves a co-ordinated complex of membrane-associated glycosyltransferases acting at the cytoplasmic face of the plasma membrane.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Glucosyl-heptosyl3-kdo2-lipid a-bisphosphoric acid
Chemical Formula:C137H254N2O68P4
Weight:Average: 3141.3503
Monoisotopic: 3139.542946482
InChI Key:JQDQBRBQZURZIG-PTTXZDEDSA-P
InChI:InChI=1S/C137H252N2O68P4/c1-7-13-19-25-31-37-38-44-50-56-62-68-100(156)189-86(66-60-54-48-42-35-29-23-17-11-5)72-102(158)194-123-104(139-98(154)71-85(65-59-53-47-41-34-28-22-16-10-4)188-99(155)67-61-55-49-43-36-30-24-18-12-6)128(186-81-95-107(161)122(193-101(157)70-84(146)64-58-52-46-40-33-27-21-15-9-3)103(129(191-95)207-211(182,183)184)138-97(153)69-83(145)63-57-51-45-39-32-26-20-14-8-2)192-96(121(123)204-208(173,174)175)82-187-136(134(169)170)74-93(201-137(135(171)172)73-87(147)105(159)116(202-137)89(149)76-141)120(119(203-136)91(151)78-143)198-132-113(167)124(126(205-209(176,177)178)117(196-132)90(150)77-142)200-133-114(168)125(199-131-112(166)108(162)106(160)94(79-144)190-131)127(206-210(179,180)181)118(197-133)92(152)80-185-130-111(165)109(163)110(164)115(195-130)88(148)75-140/h83-96,103-133,135,140-152,159-168,171-172,176-181H,7-82H2,1-6H3,(H5-2,138,139,153,154,169,170,173,174,175,182,183,184)/p+2/t83-,84-,85-,86-,87?,88?,89?,90+,91-,92+,93-,94?,95-,96-,103-,104-,105?,106?,107-,108?,109?,110?,111?,112?,113+,114+,115?,116?,117?,118?,119-,120-,121-,122-,123-,124-,125-,126-,127-,128-,129-,130?,131?,132?,133?,136-,137?/m1/s1
CAS number:Not Available
IUPAC Name:{[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-[(1R)-1,2-dihydroxyethyl]-6-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-{[(3R)-1,3-dihydroxytetradecylidene]amino}-3-hydroxy-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[(3R)-3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}oxan-3-yl]oxy}-4-{[(3S,4R,5R)-6-[(1S)-2-{[6-(1,2-dihydroxyethyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxyethyl]-3-hydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-[(trihydroxyphosphaniumyl)oxy]oxan-2-yl]oxy}-2-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-3-yl]oxy}trihydroxyphosphanium
Traditional IUPAC Name:{[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-[(1R)-1,2-dihydroxyethyl]-6-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-{[(3R)-1,3-dihydroxytetradecylidene]amino}-3-hydroxy-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[(3R)-3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}oxan-3-yl]oxy}-4-{[(3S,4R,5R)-6-[(1S)-2-{[6-(1,2-dihydroxyethyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxyethyl]-3-hydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-[(trihydroxyphosphaniumyl)oxy]oxan-2-yl]oxy}-2-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-3-yl]oxy}trihydroxyphosphanium
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])(OC4(CC([H])(O)C([H])(O)C([H])(O4)C([H])(O)CO)C(O)O)[C@@]([H])(OC4([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O[P+](O)(O)O)[C@]([H])(OC5([H])OC([H])([C@@]([H])(O)COC6([H])OC([H])(C([H])(O)CO)C([H])(O)C([H])(O)C6([H])O)[C@@]([H])(O[P+](O)(O)O)[C@]([H])(OC6([H])OC([H])(CO)C([H])(O)C([H])(O)C6([H])O)[C@]5([H])O)[C@]4([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])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C(O)C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C(O)C[C@]([H])(O)CCCCCCCCCCC
Chemical Taxonomy
Description belongs to the class of organic compounds known as saccharolipids. Saccharolipids 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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSaccharolipids
Sub ClassNot Available
Direct ParentSaccharolipids
Alternative Parents
Substituents
  • Polysaccharide
  • Saccharolipid
  • Pentacarboxylic acid or derivatives
  • Hexose phosphate
  • N-acyl-alpha-hexosamine
  • Fatty acyl glycoside
  • C-glucuronide
  • Alkyl glycoside
  • O-glycosyl compound
  • Glycosyl compound
  • C-glycosyl compound
  • Ketal
  • Monoalkyl phosphate
  • Fatty acid ester
  • Beta-hydroxy acid
  • Fatty acyl
  • Alkyl phosphate
  • Pyran
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Hydroxy acid
  • Secondary alcohol
  • Carboxylic acid ester
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Carbonyl hydrate
  • Acetal
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Organic cation
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
logP11.72ChemAxon
pKa (Strongest Acidic)0.55ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count64ChemAxon
Hydrogen Donor Count38ChemAxon
Polar Surface Area1125.24 ŲChemAxon
Rotatable Bond Count117ChemAxon
Refractivity737.25 m³·mol⁻¹ChemAxon
Polarizability334.86 ųChemAxon
Number of Rings8ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
Glucosyl-heptosyl3-KDO2-lipid A-phosphate + Adenosine triphosphate > Hydrogen ion + Glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + ADP
Glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + Uridine diphosphategalactose > Hydrogen ion + Galactosyl-glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + Uridine 5'-diphosphate
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25201743
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-935
EcoCyc IDCPD0-935

Enzymes

Protein Details
1. Lipopolysaccharide core heptose(II) kinase rfaY
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Catalyzes the phosphorylation of heptose(II) of the outer membrane lipopolysaccharide core
Gene Name:
rfaY
Uniprot ID:
P27240
Molecular weight:
27461
Protein Details
2. Lipopolysaccharide 1,6-galactosyltransferase
General function:
Involved in biosynthetic process
Specific function:
Adds a galactose goup to a glucose group of LPS
Gene Name:
rfaB
Uniprot ID:
P27127
Molecular weight:
40826