N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol (PAMDB001100)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB001100
Identification
Name: N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol
Description:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 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 Pseudomonas aeruginosa 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 Pseudomonas aeruginosa). 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.Glycosyltransferase MurG catalyses the transfer of N-acetyl-d-glucosamine to lipid intermediate I on the bacterial peptidoglycan biosynthesis pathway, and is a target for development of new antibacterial agents. (PMID 20226679)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane-D-alanyl-D-alanine-diphosphoundecaprenol
  • Lipid intermediate I
  • Lipid intermediic acid I
  • N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane-D-alanyl-D-alanine-diphosphoundecaprenol
  • Undecaprenyl-pyrophosphoryl-murnac-pentapeptide
Chemical Formula: C87H143N7O23P2
Average Molecular Weight: 1717.0469
Monoisotopic Molecular Weight: 1715.971056941
InChI Key: PNWZQTONLRRPST-OPZGOLSISA-N
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(98)75(55-95)115-87)114-70(16)82(101)89-68(14)81(100)94-74(86(107)108)51-52-76(97)93-73(50-28-49-72(88)85(105)106)83(102)90-67(13)80(99)91-69(15)84(103)104/h29,31,33,35,37,39,41,43,45,47,53,67-70,72-75,77-79,87,95,98H,18-28,30,32,34,36,38,40,42,44,46,48-52,54-55,88H2,1-17H3,(H,89,101)(H,90,102)(H,91,99)(H,92,96)(H,93,97)(H,94,100)(H,103,104)(H,105,106)(H,107,108)(H,109,110)(H,111,112)/t67-,68+,69-,70-,72-,73+,74-,75-,77-,78-,79-,87+/m1/s1
CAS number: Not Available
IUPAC Name:(2R,6S)-2-amino-6-{[(4R)-4-carboxy-1-hydroxy-4-{[(2S)-1-hydroxy-2-{[(2R)-1-hydroxy-2-{[(2R,3S,4R,5R,6S)-3-hydroxy-6-{[hydroxy({hydroxy[(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
Traditional IUPAC Name: (2R,6S)-2-amino-6-{[(4R)-4-carboxy-1-hydroxy-4-{[(2S)-1-hydroxy-2-{[(2R)-1-hydroxy-2-{[(2R,3S,4R,5R,6S)-3-hydroxy-6-({hydroxy[hydroxy(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]oxyphosphoryl}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
SMILES:[H][C@@](N)(CCC[C@]([H])(N=C(O)CC[C@@]([H])(N=C(O)[C@]([H])(C)N=C(O)[C@@]([H])(C)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO)O[C@@]([H])(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)[C@]1([H])N=C(C)O)C(O)=O)C(O)=N[C@]([H])(C)C(O)=N[C@]([H])(C)C(O)=O)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it.
Kingdom Organic compounds
Super ClassLipids and lipid-like molecules
Class Prenol lipids
Sub ClassPolyprenols
Direct Parent Polyprenyl phospho carbohydrates
Alternative Parents
Substituents
  • Polyterpenoid
  • Bactoprenol diphosphate
  • Polyprenyl phospho carbohydrate
  • Alpha peptide
  • Saccharolipid
  • N-acyl-alpha-hexosamine
  • N-acyl-aliphatic-alpha amino acid
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Glucosamine
  • Amino sugar
  • L-alpha-amino acid
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Isoprenoid phosphate
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Monoalkyl phosphate
  • Amino saccharide
  • Amino fatty acid
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Saccharide
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-4
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.00186 mg/mLALOGPS
logP3.71ALOGPS
logP16.7ChemAxon
logS-6ALOGPS
pKa (Strongest Acidic)1.72ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count27ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area494.67 Å2ChemAxon
Rotatable Bond Count60ChemAxon
Refractivity469.28 m3·mol-1ChemAxon
Polarizability191.19 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol + Uridine diphosphate-N-acetylglucosamine <> Hydrogen ion + N-Acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + Uridine 5'-diphosphate
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine + Di-trans,poly-cis-undecaprenyl phosphate > N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol + Uridine 5'-monophosphate
Pathways: Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-1011139200-a5086b1fa04a83dc0d2bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-3130033911-ab862a3d1358e36e1757View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001d-9333332400-1bd354ac67fc3da0fbdcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-06vj-3000039507-bfb6f7440faf705b9965View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052b-3300018109-4bce894814e4eb3aa402View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-6910002002-df1a7b3aba2e08f6af47View in MoNA
References
References:
  • 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
  • Trunkfield, A. E., Gurcha, S. S., Besra, G. S., Bugg, T. D. (2010). "Inhibition of Escherichia coli glycosyltransferase MurG and Mycobacterium tuberculosis Gal transferase by uridine-linked transition state mimics." Bioorg Med Chem 18:2651-2663. Pubmed: 20226679
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25200588
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDC5
EcoCyc IDC5

Enzymes

Protein Details
• Phospho-N-acetylmuramoyl-pentapeptide-transferase
General function:
Involved in phospho-N-acetylmuramoyl-pentapeptide-transferase activity
Specific function:
First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
Gene Name:
mraY
Locus Tag:
PA4415
Molecular weight:
39.7 kDa
Reactions
UDP-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate = UMP + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.
Protein Details
• UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
General function:
Involved in undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity
Specific function:
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
Gene Name:
murG
Locus Tag:
PA4412
Molecular weight:
37.8 kDa
Reactions
UDP-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = UDP + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.

Transporters