2.02012-05-31 14:55:18 -06002015-06-03 17:20:27 -0600ECMDB21031M2MDB001447KDO2-Lipid AKDO2-Lipid A is an intermediate in the synthesis of LPS. It has two 3-deoxy-D-manno-octulosonic acid (KDO) sugar residues in place of the core, and has no O-antigen. α-Kdo-(2→4)-α-Kdo-(2→6)-lipid Aa-kdo-(2->4)-a-kdo-(2->6)-lipid aAlpha-KDO-(2->4)-alpha-KDO-(2->6)-lipid ARe endotoxinα-kdo-(2->4)-α-kdo-(2->6)-lipid aC110H202N2O39P22238.71842237.335997756(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]-2-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-[(1,3-dihydroxytetradecylidene)amino]-3-hydroxy-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxane-2-carboxylic acid(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]-2-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-[(1,3-dihydroxytetradecylidene)amino]-3-hydroxy-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxane-2-carboxylic acid[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])(O)[C@]([H])(O3)[C@]([H])(O)CO)C(O)=O)[C@@]([H])(OP(O)(O)=O)[C@]([H])(OC(=O)CC([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C(O)CC([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C(O)CC([H])(O)CCCCCCCCCCCInChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/t79?,80?,81?,82?,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1DIXUKJUHGLIZGU-ZKUMOPDFSA-NCytosolExtra-organismMembranePeriplasmlogp4.35logs-5.08solubility1.86e-02 g/llogp22.64pka_strongest_acidic0.55iupac(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]-2-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-[(1,3-dihydroxytetradecylidene)amino]-3-hydroxy-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxane-2-carboxylic acidaverage_mass2238.7184mono_mass2237.335997756smiles[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])(O)[C@]([H])(O3)[C@]([H])(O)CO)C(O)=O)[C@@]([H])(OP(O)(O)=O)[C@]([H])(OC(=O)CC([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C(O)CC([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C(O)CC([H])(O)CCCCCCCCCCCformulaC110H202N2O39P2inchiInChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/t79?,80?,81?,82?,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1inchikeyDIXUKJUHGLIZGU-ZKUMOPDFSA-Npolar_surface_area645.41refractivity564.64polarizability249.16rotatable_bond_count98acceptor_count35donor_count18physiological_charge-5formal_charge0Lipopolysaccharide biosynthesisE. coli lipid A is synthesized on the cytoplasmic surface of the inner membrane. The pathway can start from the fructose 6-phosphate that is either produced in the glycolysis and pyruvate dehydrogenase or be obtained from the interaction with D-fructose interacting with a mannose PTS permease. Fructose 6-phosphate interacts with L-glutamine through a D-fructose-6-phosphate aminotransferase resulting into a L-glutamic acid and a glucosamine 6-phosphate. The latter compound is isomerized through a phosphoglucosamine mutase resulting a glucosamine 1-phosphate. This compound is acetylated, interacting with acetyl-CoA through a bifunctional protein glmU resulting in a Coenzyme A, hydrogen ion and N-acetyl-glucosamine 1-phosphate. This compound interact with UTP and hydrogen ion through the bifunctional protein glmU resulting in a pyrophosphate and a UDP-N-acetylglucosamine. This compound interacts with (3R)-3-hydroxymyristoyl-[acp] through an UDP-N-acetylglucosamine acyltransferase resulting in a holo-[acp] and a UDP-3-O[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine. This compound interacts with water through UDP-3-O-acyl-N-acetylglucosamine deacetylase resulting in an acetic acid and UDP-3-O-(3-hydroxymyristoyl)-α-D-glucosamine. The latter compound interacts with (3R)-3-hydroxymyristoyl-[acp] through
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase releasing a hydrogen ion, a holo-acp and UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine. The latter compound is hydrolase by interacting with water and a UDP-2,3-diacylglucosamine hydrolase resulting in UMP, hydrogen ion and 2,3-bis[(3R)-3-hydroxymyristoyl]-α-D-glucosaminyl 1-phosphate. This last compound then interacts with a UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine through a lipid A disaccharide synthase resulting in a release of UDP, hydrogen ion and a lipid A disaccharide. The lipid A disaccharide is phosphorylated by an ATP mediated
tetraacyldisaccharide 4'-kinase resulting in the release of hydrogen ion and lipid IVA.
A D-ribulose 5-phosphate is isomerized with D-arabinose 5-phosphate isomerase 2 to result in a D-arabinose 5-phosphate. This compounds interacts with water and phosphoenolpyruvic acid through a 3-deoxy-D-manno-octulosonate 8-phosphate synthase resulting in the release of phosphate and 3-deoxy-D-manno-octulosonate 8-phosphate. This compound interacts with water through a 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase thus releasing a phosphate and a 3-deoxy-D-manno-octulosonate. The latter compound interacts with CTP through a 3-deoxy-D-manno-octulosonate cytidylyltransferase resulting in a pyrophosphate and
CMP-3-deoxy-α-D-manno-octulosonate.
CMP-3-deoxy-α-D-manno-octulosonate and lipid IVA interact with each other through a KDO transferase resulting in CMP, hydrogen ion and alpha-Kdo-(2-->6)-lipid IVA. The latter compound reacts with CMP-3-deoxy-α-D-manno-octulosonate through a KDO transferase resulting in a CMP, hydrogen ion, and a a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA. The latter compound interacts with a dodecanoyl-[acp] lauroyl acyltransferase resulting in a holo-[acp] and a (KDO)2-(lauroyl)-lipid IVA. The latter compound reacts with a myristoyl-[acp] through a myristoyl-acyl carrier protein (ACP)-dependent acyltransferase resulting in a holo-[acp], (KDO)2-lipid A. The latter compound reacts with ADP-L-glycero-beta-D-manno-heptose through ADP-heptose:LPS heptosyltransferase I resulting hydrogen ion, ADP, heptosyl-KDO2-lipid A. The latter compound interacts with ADP-L-glycero-beta-D-manno-heptose through ADP-heptose:LPS heptosyltransferase II resulting in ADP, hydrogen ion and (heptosyl)2-Kdo2-lipid A. The latter compound UDP-glucose interacts with (heptosyl)2-Kdo2-lipid A resulting in UDP, hydrogen ion and glucosyl-(heptosyl)2-Kdo2-lipid A. Glucosyl-(heptosyl)2-Kdo2-lipid A (Escherichia coli) is phosphorylated through an ATP-mediated lipopolysaccharide core heptose (I) kinase resulting in ADP, hydrogen ion and glucosyl-(heptosyl)2-Kdo2-lipid A-phosphate.
The latter compound interacts with ADP-L-glycero-beta-D-manno-heptose through a lipopolysaccharide core heptosyl transferase III resulting in ADP, hydrogen ion, and glucosyl-(heptosyl)3-Kdo2-lipid A-phosphate. The latter compound is phosphorylated through an ATP-driven lipopolysaccharide core heptose (II) kinase resulting in ADP, hydrogen ion and glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate. The latter compound interacts with UDP-alpha-D-galactose through a UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase resulting in a UDP, a hydrogen ion and a galactosyl-glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate. The latter compound interacts with UDP-glucose through a (glucosyl)LPS α-1,3-glucosyltransferase resulting in a hydrogen ion, a UDP and galactosyl-(glucosyl)2-(heptosyl)3-Kdo2-lipid A-bisphosphate. This compound then interacts with UDP-glucose through a UDP-glucose:(glucosyl)LPS α-1,2-glucosyltransferase resulting in UDP, a hydrogen ion and galactosyl-(glucosyl)3-(heptosyl)3-Kdo2-lipid A-bisphosphate. This compound then interacts with ADP-L-glycero-beta-D-manno-heptose through a lipopolysaccharide core biosynthesis; heptosyl transferase IV; probably hexose transferase resulting in a Lipid A-core.
A lipid A-core is then exported into the periplasmic space by a lipopolysaccharide ABC transporter.
The lipid A-core is then flipped to the outer surface of the inner membrane by the ATP-binding cassette (ABC) transporter, MsbA. An additional integral membrane protein, YhjD, has recently been implicated in LPS export across the IM. The smallest LPS derivative that supports viability in E. coli is lipid IVA. However, it requires mutations in either MsbA or YhjD, to suppress the normally lethal consequence of an incomplete lipid A . Recent studies with deletion mutants implicate the periplasmic protein LptA, the cytosolic protein LptB, and the IM proteins LptC, LptF, and LptG in the subsequent transport of nascent LPS to the outer membrane (OM), where the LptD/LptE complex flips LPS to the outer surface. PW000831ec00540MetabolicCationic antimicrobial peptide (CAMP) resistanceeco01503polymyxin resistancePWY0-1338Lipid A-core biosynthesisLIPA-CORESYN-PWYsuperpathway of (KDO)<SUB>2</SUB>-lipid A biosynthesisKDO-NAGLIPASYN-PWY(KDO)<sub>2</sub>-lipid A biosynthesis IKDO-LIPASYN-PWYsuperpathway of lipopolysaccharide biosynthesisLPSSYN-PWYSpecdb::MsMs3640587Specdb::MsMs3640588Specdb::MsMs3640589Specdb::MsMs3640590Specdb::MsMs3640591Specdb::MsMs3640592440886389718C0602627963KDO2-LIPID-AKeseler, 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-D590.21097882Kanehisa, 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-D114.22080510van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25.17765195Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948.18331064Lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferaseP24205MSBB_ECOLImsbBhttp://ecmdb.ca/proteins/P24205.xmlPhosphoethanolamine transferase eptBP37661EPTB_ECOLIeptBhttp://ecmdb.ca/proteins/P37661.xmlUndecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferaseP76473ARNT_ECOLIarnThttp://ecmdb.ca/proteins/P76473.xmlLipopolysaccharide heptosyltransferase 1P24173RFAC_ECOLIrfaChttp://ecmdb.ca/proteins/P24173.xmlLipopolysaccharide export system permease protein lptGP0ADC6LPTG_ECOLIlptGhttp://ecmdb.ca/proteins/P0ADC6.xmlLipopolysaccharide export system permease protein lptFP0AF98LPTF_ECOLIlptFhttp://ecmdb.ca/proteins/P0AF98.xmlLipid A export ATP-binding/permease protein msbAP60752MSBA_ECOLImsbAhttp://ecmdb.ca/proteins/P60752.xmlLipopolysaccharide export system ATP-binding protein lptBP0A9V1LPTB_ECOLIlptBhttp://ecmdb.ca/proteins/P0A9V1.xmlProtein crcAP37001CRCA_ECOLIcrcAhttp://ecmdb.ca/proteins/P37001.xmlLipopolysaccharide export system protein lptCP0ADV9LPTC_ECOLIlptChttp://ecmdb.ca/proteins/P0ADV9.xmlLipopolysaccharide export system protein lptAP0ADV1LPTA_ECOLIlptAhttp://ecmdb.ca/proteins/P0ADV1.xmlLipopolysaccharide export system permease protein lptGP0ADC6LPTG_ECOLIlptGhttp://ecmdb.ca/proteins/P0ADC6.xmlLipopolysaccharide export system permease protein lptFP0AF98LPTF_ECOLIlptFhttp://ecmdb.ca/proteins/P0AF98.xmlLipid A export ATP-binding/permease protein msbAP60752MSBA_ECOLImsbAhttp://ecmdb.ca/proteins/P60752.xmlAdenosine triphosphate + Water + KDO2-Lipid A > ADP + Hydrogen ion + Phosphate + KDO2-Lipid AAdenosine triphosphate + Water + KDO2-Lipid A > ADP + Hydrogen ion + Phosphate + KDO2-Lipid AHydrogen ion + Palmitic acid + KDO2-Lipid A > Water + Hepta-acylated KDO2-lipid AAdenosine triphosphate + Water + KDO2-Lipid A > ADP + Hydrogen ion + Phosphate + KDO2-Lipid AAdenosine triphosphate + Water + KDO2-Lipid A > ADP + Hydrogen ion + Phosphate + KDO2-Lipid AKDO(2)-lipid IV(A) with laurate + Myristoyl-ACP (n-C14:0ACP) > acyl carrier protein + KDO2-Lipid AKDO2-Lipid A + PE(14:0/14:0) > 1,2-Diacyl-sn-glycerol (dihexadec-9-enoyl, n-C16:1) + Phosphoethanolamine KDO(2)-lipid (A)KDO2-Lipid A + PE(14:0/14:0) > 1,2-Diacyl-sn-glycerol (dioctadec-11-enoyl, n-C18:1) + Phosphoethanolamine KDO(2)-lipid (A)ADP-L-Glycero-D-manno-heptose + KDO2-Lipid A > ADP + Hydrogen ion + heptosyl-kdo2-lipidAKDO2-Lipid A + Acyl-carrier protein + Tetradecanoyl-[acp] + Lauroyl-KDO2-lipid IV(A) <> Tetradecanoyl-[acp] + Lauroyl-KDO2-lipid IV(A) + Acyl-carrier proteinR05075a phospholipid + KDO2-Lipid A > a glycerol ester + Hepta-acylated KDO2-lipid ARXN0-1842KDO2-Lipid A + 4-amino-4-deoxy-α-L-arabinopyranosyl <i>ditrans,octacis</i>-undecaprenyl phosphate > L-Ara4N-modified KDO2-Lipid A + Di-trans,poly-cis-undecaprenyl phosphateRXN0-2001Hydrogen ion + KDO2-Lipid A + ADP-L-Glycero-D-manno-heptose > Heptosyl-KDO2-lipid A + ADPRXN0-5118undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose + KDO2-Lipid A + 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate <> alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-[4-P-L-Ara4N]-lipid A + Di-trans,poly-cis-undecaprenyl phosphate + Lipid IIAR09781 undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose + KDO2-Lipid A + 2 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate <> alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-[4-P-L-Ara4N]-lipid A + Di-trans,poly-cis-undecaprenyl phosphate + Lipid IIA