2.0 2012-05-31 14:33:38 -0600 2015-09-17 15:42:07 -0600 ECMDB20216 M2MDB001062 Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is an intermediate in peptidoglycan synthesis. It is a substrate for the enzyme undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase (murG). Peptidoglycan can be described as a fisherman's net that encloses bacteria. The mesh of the net is made of two segments of parallel, somewhat inextensible glycan threads, held together by two small elastic peptide crosslinks allowing the net to expand or shrink. The glycan moiety of the peptidoglycan is very uniform among all bacteria, and is made up of alternating β-1,4-linked N-acetylglucosamine and N-acetyl muramate residues, with an average chain lengthof 10 to 65 disaccharide units (depending on the organism). The peptidoglycan synthesis pathway starts in the cytoplasm, where in six steps the peptidoglycan precursor a UDP-N-acetylmuramoyl-pentapeptide is synthesized. This precursor is then attached to the memberane acceptor all-trans-undecaprenyl phosphate, generating a N-acetylmuramoyl-pentapeptide-diphosphoundecaprenol, also known as lipid I. Another transferase then adds UDP-N-acetyl-α-D-glucosamine, yielding the complete monomeric unit a lipid II, also known as lipid II. This final lipid intermediate is transferred by an as yet unknown mechanism through the membrane. The peptidoglycan monomers are then polymerized on the outside surface by glycosyltransferases, which form the linear glycan chains, and transpeptidases, which catalyze the formation of peptide crosslinks. Peptide crosslinks form between different parts of the peptides depending on the organism. For example, in Mycobacteria and in E. coli most links form between the carboxyl group of the penultimate D-alanine (residue 4) of one peptide to the amino group at the D-center of meso-diaminopimelate (residue 3) of an adjacent peptide of a second glycan chain (as in E. coli). The crosslinking reaction is catalyzed by transpeptidases and involves the cleavage of the D-alanyl-D-alanine bond of the donor peptide, providing the energy to drive the reaction. As a result, the peptides in the peptidoglycan polymers are one or two amino acids shorter than the peptides in the monomers. MurNAcAlaGludAHeAlaAdePPUn UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine UDP-n-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioic acid- D-alanyl-D-alanine UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioic acid- D-alanyl-D-alanine UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine C87H139N7O23P2 1713.045 1711.941952079 (2S,6R)-2-amino-6-{[(2R)-4-carboxy-1-hydroxy-2-{[(2S)-1-hydroxy-2-[(1-hydroxy-2-{[(2R,3S,4R,5R,6R)-3-hydroxy-6-{[hydroxy({[hydroxy({[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}-5-[(1-hydroxyethylidene)amino]-2-(hydroxymethyl)oxan-4-yl]oxy}propylidene)amino]propylidene]amino}butylidene]amino}-6-{[(1R)-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}hexanoic acid (2S,6R)-2-amino-6-{[(2R)-4-carboxy-1-hydroxy-2-{[(2S)-1-hydroxy-2-[(1-hydroxy-2-{[(2R,3S,4R,5R,6R)-3-hydroxy-6-{[hydroxy({hydroxy[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxyphosphoryl}oxy)phosphoryl]oxy}-5-[(1-hydroxyethylidene)amino]-2-(hydroxymethyl)oxan-4-yl]oxy}propylidene)amino]propylidene]amino}butylidene]amino}-6-{[(1R)-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}hexanoic acid CC(NC(=O)C(C)NC(=O)C(CCCC([NH3+])C([O-])=O)NC(=O)C(CCC([O-])=O)NC(=O)C(C)NC(=O)C(C)OC1C(O)C(CO)OC(OP([O-])(=O)OP([O-])(=O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)C1NC(C)=O)C([O-])=O InChI=1S/C87H143N7O23P2/c1-56(2)29-18-30-57(3)31-19-32-58(4)33-20-34-59(5)35-21-36-60(6)37-22-38-61(7)39-23-40-62(8)41-24-42-63(9)43-25-44-64(10)45-26-46-65(11)47-27-48-66(12)53-54-113-118(109,110)117-119(111,112)116-87-77(92-71(17)96)79(78(99)75(55-95)115-87)114-70(16)82(102)89-68(14)81(101)93-74(51-52-76(97)98)84(104)94-73(50-28-49-72(88)86(107)108)83(103)90-67(13)80(100)91-69(15)85(105)106/h29,31,33,35,37,39,41,43,45,47,53,67-70,72-75,77-79,87,95,99H,18-28,30,32,34,36,38,40,42,44,46,48-52,54-55,88H2,1-17H3,(H,89,102)(H,90,103)(H,91,100)(H,92,96)(H,93,101)(H,94,104)(H,97,98)(H,105,106)(H,107,108)(H,109,110)(H,111,112)/p-4 QSVYTJPCVMYPIS-UHFFFAOYSA-J Membrane logp 3.67 ALOGPS logs -5.95 ALOGPS solubility 1.91e-03 g/l ALOGPS logp 16.7 ChemAxon pka_strongest_acidic 1.72 ChemAxon iupac (2S,6R)-2-amino-6-{[(2R)-4-carboxy-1-hydroxy-2-{[(2S)-1-hydroxy-2-[(1-hydroxy-2-{[(2R,3S,4R,5R,6R)-3-hydroxy-6-{[hydroxy({[hydroxy({[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}-5-[(1-hydroxyethylidene)amino]-2-(hydroxymethyl)oxan-4-yl]oxy}propylidene)amino]propylidene]amino}butylidene]amino}-6-{[(1R)-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}hexanoic acid ChemAxon average_mass 1713.045 ChemAxon mono_mass 1711.941952079 ChemAxon smiles CC(NC(=O)C(C)NC(=O)C(CCCC([NH3+])C([O-])=O)NC(=O)C(CCC([O-])=O)NC(=O)C(C)NC(=O)C(C)OC1C(O)C(CO)OC(OP([O-])(=O)OP([O-])(=O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)C1NC(C)=O)C([O-])=O ChemAxon formula C87H139N7O23P2 ChemAxon inchi InChI=1S/C87H143N7O23P2/c1-56(2)29-18-30-57(3)31-19-32-58(4)33-20-34-59(5)35-21-36-60(6)37-22-38-61(7)39-23-40-62(8)41-24-42-63(9)43-25-44-64(10)45-26-46-65(11)47-27-48-66(12)53-54-113-118(109,110)117-119(111,112)116-87-77(92-71(17)96)79(78(99)75(55-95)115-87)114-70(16)82(102)89-68(14)81(101)93-74(51-52-76(97)98)84(104)94-73(50-28-49-72(88)86(107)108)83(103)90-67(13)80(100)91-69(15)85(105)106/h29,31,33,35,37,39,41,43,45,47,53,67-70,72-75,77-79,87,95,99H,18-28,30,32,34,36,38,40,42,44,46,48-52,54-55,88H2,1-17H3,(H,89,102)(H,90,103)(H,91,100)(H,92,96)(H,93,101)(H,94,104)(H,97,98)(H,105,106)(H,107,108)(H,109,110)(H,111,112)/p-4 ChemAxon inchikey QSVYTJPCVMYPIS-UHFFFAOYSA-J ChemAxon polar_surface_area 494.67 ChemAxon refractivity 469.28 ChemAxon polarizability 190.99 ChemAxon rotatable_bond_count 60 ChemAxon acceptor_count 27 ChemAxon donor_count 14 ChemAxon physiological_charge -4 ChemAxon formal_charge 0 ChemAxon Peptidoglycan biosynthesis ec00550 peptidoglycan biosynthesis I Peptidoglycan is a net-like polymer which surrounds the cytoplasmic membrane of most bacteria and functions to maintain cell shape and prevent rupture due to the internal turgor.In E. coli K-12, the peptidoglycan consists of glycan strands of alternating subunits of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) which are cross-linked by short peptides. The pathway for constructing this net involves two cell compartments: cytoplasm and periplasmic space. The pathway starts with a beta-D-fructofuranose going through a mannose PTS permease, phosphorylating the compund and producing a beta-D-fructofuranose 6 phosphate. This compound can be obtained from the glycolysis and pyruvate dehydrogenase or from an isomerization reaction of Beta-D-glucose 6-phosphate through a glucose-6-phosphate isomerase.The compound Beta-D-fructofuranose 6 phosphate and L-Glutamine react with a glucosamine fructose-6-phosphate aminotransferase, thus producing a glucosamine 6-phosphate and a l-glutamic acid. The glucosamine 6-phosphate interacts with phosphoglucosamine mutase in a reversible reaction producing glucosamine-1P. Glucosamine-1p and acetyl coa undergo acetylation throuhg a bifunctional protein glmU releasing Coa and a hydrogen ion and producing a N-acetyl-glucosamine 1-phosphate. Glmu, being a bifunctional protein, follows catalyze the interaction of N-acetyl-glucosamine 1-phosphate, hydrogen ion and UTP into UDP-N-acetylglucosamine and pyrophosphate. UDP-N-acetylglucosamine then interacts with phosphoenolpyruvic acid and a UDP-N acetylglucosamine 1- carboxyvinyltransferase realeasing a phosphate and the compound UDP-N-acetyl-alpha-D-glucosamine-enolpyruvate. This compound undergoes a NADPH dependent reduction producing a UDP-N-acetyl-alpha-D-muramate through a UDP-N-acetylenolpyruvoylglucosamine reductase. UDP-N-acetyl-alpha-D-muramate and L-alanine react in an ATP-mediated ligation through a UDP-N-acetylmuramate-alanine ligase releasing an ADP, hydrogen ion, a phosphate and a UDP-N-acetylmuramoyl-L-alanine. This compound interacts with D-glutamic acid and ATP through UDP-N-acetylmuramoylalanine-D-glutamate ligase releasing ADP, A phosphate and UDP-N-acetylmuramoyl-L-alanyl-D-glutamate. The latter compound then interacts with meso-diaminopimelate in an ATP mediated ligation through a UDP-N-acetylmuramoylalanine-D-glutamate-2,6-diaminopimelate ligase resulting in ADP, phosphate, hydrogen ion and UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate. This compound in turn with D-alanyl-D-alanine react in an ATP-mediated ligation through UDP-N-Acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase to produce UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine and hydrogen ion, ADP, phosphate. UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine interacts with di-trans,octa-cis-undecaprenyl phosphate through a phospho-N-acetylmuramoyl-pentapeptide-transferase, resulting in UMP and Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine which in turn reacts with a UDP-N-acetylglucosamine through a N-acetylglucosaminyl transferase to produce a hydrogen, UDP and ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine. This compound ends the cytoplasmic part of the pathway. ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is transported through a lipi II flippase. Once in the periplasmic space, the compound reacts with a penicillin binding protein 1A prodducing a peptidoglycan dimer, a hydrogen ion, and UDP. The peptidoglycan dimer then reacts with a penicillin binding protein 1B producing a peptidoglycan with D,D, cross-links and a D-alanine. PW000906 Metabolic UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-DAP-containing) PWY-6387 peptidoglycan biosynthesis I (meso-diaminopimelate containing) PEPTIDOGLYCANSYN-PWY Specdb::MsMs 26975 Specdb::MsMs 26976 Specdb::MsMs 26977 Specdb::MsMs 33533 Specdb::MsMs 33534 Specdb::MsMs 33535 23724491 C05897 C1 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. 21097882 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. 22080510 Phospho-N-acetylmuramoyl-pentapeptide-transferase P0A6W3 MRAY_ECOLI mraY http://ecmdb.ca/proteins/P0A6W3.xml UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase P17443 MURG_ECOLI murG http://ecmdb.ca/proteins/P17443.xml Undecaprenyl phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine > Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-monophosphate Uridine diphosphate-N-acetylglucosamine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine > Hydrogen ion + Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-diphosphate R05032 Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine diphosphate-N-acetylglucosamine <> Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-diphosphate R05032 UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine + Di-trans,poly-cis-undecaprenyl phosphate <> Uridine 5'-monophosphate + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine R05630 UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + di-trans,octa-cis-undecaprenyl phosphate > Uridine 5'-monophosphate + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine PW_R003452 Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine diphosphate-N-acetylglucosamine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine > Uridine 5'-diphosphate + Hydrogen ion + lipid II(A) + Uridine 5'-diphosphate PW_R003453