P. aeruginosa Metabolome Database: Lipid A-core (PAMDB001343)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB001343

Identification

Name:

Lipid A-core

Description:

Lipid a-core belongs to the class of Polyhexoses. These are polysaccharides in which the saccharide units are hexoses. (inferred from compound structure) Lipopolysaccharide (LPS) is a major component on the surface of Gram negative bacteria and is composed of lipid A-core and the O antigen polysaccharide. (PMID 20333251) WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. (PMID 19019161) MsbA is an essential ATP-binding cassette half-transporter in the cytoplasmic membrane of the gram-negative Pseudomonas aeruginosa and is required for the export of lipopolysaccharides (LPS) to the outer membrane, most likely by transporting the lipid A core moiety. (PMID 16159769)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

Not Available

Chemical Formula:

C₁₆₂H₂₉₆N₂O₈₉P₄

Average Molecular Weight:

3819.9387

Monoisotopic Molecular Weight:

3817.764804888

InChI Key:

PIKXVLIJAUWPDI-VUQADABISA-P

InChI:

InChI=1S/C162H294N2O89P4/c1-7-13-19-25-31-37-38-44-50-56-62-68-108(184)229-90(66-60-54-48-42-35-29-23-17-11-5)72-110(186)237-142-112(164-106(182)71-89(65-59-53-47-41-34-28-22-16-10-4)228-107(183)67-61-55-49-43-36-30-24-18-12-6)149(224-84-102-117(191)141(236-109(185)70-88(173)64-58-52-46-40-33-27-21-15-9-3)111(150(232-102)253-257(220,221)222)163-105(181)69-87(172)63-57-51-45-39-32-26-20-14-8-2)235-104(140(142)250-254(211,212)213)86-227-161(159(207)208)74-98(247-162(160(209)210)73-91(174)113(187)135(248-162)94(177)77-167)139(138(249-161)96(179)79-169)242-156-131(205)144(147(251-255(214,215)216)136(240-156)95(178)78-168)245-157-132(206)145(148(252-256(217,218)219)137(241-157)97(180)82-223-152-127(201)121(195)124(198)133(238-152)92(175)75-165)244-155-130(204)143(118(192)103(234-155)85-225-151-126(200)119(193)114(188)99(80-170)230-151)243-158-146(123(197)115(189)100(81-171)231-158)246-154-129(203)120(194)116(190)101(233-154)83-226-153-128(202)122(196)125(199)134(239-153)93(176)76-166/h87-104,111-158,160,165-180,187-206,209-210,214-219H,7-86H2,1-6H3,(H5-2,163,164,181,182,207,208,211,212,213,220,221,222)/p+2/t87-,88-,89-,90-,91-,92+,93+,94-,95+,96-,97+,98-,99-,100-,101-,102-,103-,104-,111-,112-,113-,114+,115-,116-,117-,118-,119+,120+,121+,122+,123+,124+,125+,126-,127+,128+,129-,130-,131+,132+,133?,134?,135-,136?,137?,138-,139-,140-,141-,142-,143?,144-,145-,146?,147-,148-,149-,150-,151?,152?,153?,154?,155?,156?,157?,158?,161-,162-/m1/s1

CAS number:

Not Available

IUPAC Name:

{[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-2-[(1R)-1,2-dihydroxyethyl]-4-{[(2R,4R,5R,6R)-6-[(1R)-1,2-dihydroxyethyl]-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-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}-2-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4R,5R)-6-[(1S)-2-{[(3S,4S,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxyethyl]-4-{[(3R,5R,6R)-4-{[(4S,5S,6R)-3-{[(3R,4S,5S,6R)-6-({[(3S,4S,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-3-hydroxy-5-[(trihydroxyphosphaniumyl)oxy]oxan-2-yl]oxy}-5-hydroxyoxan-3-yl]oxy}trihydroxyphosphanium

Traditional IUPAC Name:

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])(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)[C@]6([H])O)[C@@]([H])(O[P+](O)(O)O)[C@]([H])(OC6([H])O[C@]([H])(COC7([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O)[C@@]7([H])O)[C@@]([H])(O)C([H])(OC7([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)C7([H])OC7([H])O[C@]([H])(COC8([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O)[C@]([H])(O)[C@]8([H])O)[C@@]([H])(O)[C@]([H])(O)[C@@]7([H])O)[C@@]6([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

Taxonomy Description

This compound belongs to the class of organic compounds known as polysaccharides. These are compounds containing more than ten saccharide units.

Kingdom

Organic compounds

Super Class

Organic Polymers

Class

Polysaccharides

Sub Class

Not Available

Direct Parent

Polysaccharides

Alternative Parents

Substituents

Polysaccharide
Saccharolipid
Hexose phosphate
Pentacarboxylic acid or derivatives
Fatty acyl glycoside
N-acyl-alpha-hexosamine
C-glucuronide
Alkyl glycoside
O-glycosyl compound
C-glycosyl compound
Glycosyl compound
Pyran carboxylic acid
Pyran carboxylic acid or derivatives
Fatty acid ester
Monoalkyl phosphate
Ketal
Beta-hydroxy acid
Hydroxy acid
Phosphoric acid ester
Pyran
Alkyl phosphate
Fatty acyl
Organic phosphoric acid derivative
Organic phosphate
1,2-diol
Carboxylic acid ester
Secondary alcohol
Polyol
Oxacycle
Organoheterocyclic compound
1,1-diol
Carboxylic acid
Acetal
Carboxylic acid derivative
Carboximidic acid derivative
Organonitrogen compound
Carbonyl group
Organic cation
Alcohol
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
logP	4.01	ChemAxon
pKa (Strongest Acidic)	0.55	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	85	ChemAxon
Hydrogen Donor Count	51	ChemAxon
Polar Surface Area	1462.07 Å²	ChemAxon
Rotatable Bond Count	130	ChemAxon
Refractivity	872.87 m³·mol^-1	ChemAxon
Polarizability	396 Å³	ChemAxon
Number of Rings	12	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Membrane

Reactions:

Lipid A-core + colanic acid > M<sub>LPS</sub>
Galactosyl-glucosyl3-heptosyl3-KDO2-lipid A-bisphosphate + ADP-L-Glycero-D-manno-heptose > Hydrogen ion + Lipid A-core + ADP
galactosyl-(glucosyl)3-(heptosyl)3-Kdo2-lipid A-bisphosphate + ADP-L-glycero-beta-D-manno-heptose > Hydrogen ion + Adenosine diphosphate + Lipid A-core + ADP
Lipid A-core + Adenosine triphosphate + Water > Adenosine diphosphate + Phosphate + Hydrogen ion + Lipid A-core + ADP
Lipid A-core + Adenosine triphosphate + Water > Adenosine diphosphate + Phosphate + Hydrogen ion + Lipid A-core + ADP

Pathways:

Lipopolysaccharide biosynthesis pae00540

Spectra

Spectra:

References

References:

Hug, I., Couturier, M. R., Rooker, M. M., Taylor, D. E., Stein, M., Feldman, M. F. (2010). "Helicobacter pylori lipopolysaccharide is synthesized via a novel pathway with an evolutionary connection to protein N-glycosylation." PLoS Pathog 6:e1000819. Pubmed: 20333251
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
Perez, J. M., McGarry, M. A., Marolda, C. L., Valvano, M. A. (2008). "Functional analysis of the large periplasmic loop of the Escherichia coli K-12 WaaL O-antigen ligase." Mol Microbiol 70:1424-1440. Pubmed: 19019161
Woebking, B., Reuter, G., Shilling, R. A., Velamakanni, S., Shahi, S., Venter, H., Balakrishnan, L., van Veen, H. W. (2005). "Drug-lipid A interactions on the Escherichia coli ABC transporter MsbA." J Bacteriol 187:6363-6369. Pubmed: 16159769

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	25202953
Kegg ID	Not Available
ChemSpider ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	CPD0-939
EcoCyc ID	CPD0-939

Enzymes

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

Transporters

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

Lipid A-core (PAMDB001343)

Structure for Lipid A-core (PAMDB001343)

Enzymes

Transporters