P. aeruginosa Metabolome Database: KDO-lipid IV(A) (PAMDB001644)

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

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB001644

Identification

Name:

KDO-lipid IV(A)

Description:

KDO-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 Pseudomonas aeruginosa is Kdo2-Lipid A, a hexa-acylated disaccharide of glucosamine that is glycosylated with two 3-deoxy-D-manno-octulosonic acid (Kdo) residues.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

(KDO)-lipid IV_A
(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

Average Molecular Weight:

1625.8836

Monoisotopic Molecular Weight:

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

Taxonomy Description

This 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 Class

Lipids and lipid-like molecules

Class

Saccharolipids

Sub Class

Not Available

Direct Parent

Saccharolipids

Alternative Parents

Substituents

Saccharolipid
N-acyl-alpha-hexosamine
Disaccharide phosphate
C-glucuronide
Glucosamine
Amino sugar
O-glycosyl compound
Glycosyl compound
Disaccharide
C-glycosyl compound
Tricarboxylic acid or derivatives
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
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

lipid As (CHEBI:27439 )

Physical Properties

State:

Not Available

Charge:

-5

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.04 mg/mL	ALOGPS
logP	3.72	ALOGPS
logP	11.31	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	0.6	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	26	ChemAxon
Hydrogen Donor Count	16	ChemAxon
Polar Surface Area	509.84 Å²	ChemAxon
Rotatable Bond Count	67	ChemAxon
Refractivity	400.81 m³·mol^-1	ChemAxon
Polarizability	178.81 Å³	ChemAxon
Number of Rings	3	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:

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 + α-Kdo-(2->4)-α-Kdo-(2->6)-lipid IV<SUB>A</SUB> + Cytidine monophosphate

Pathways:

Lipopolysaccharide biosynthesis pae00540

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

Links

External Links:

Resource	Link
CHEBI ID	27439
HMDB ID	Not Available
Pubchem Compound ID	819
Kegg ID	C06024
ChemSpider ID	26333135
Wikipedia ID	Not Available
BioCyc ID	KDO-LIPID-IVA
EcoCyc ID	KDO-LIPID-IVA

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

KDO-lipid IV(A) (PAMDB001644)

Structure for KDO-lipid IV(A) (PAMDB001644)

Enzymes