UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate (ECMDB04169) (M2MDB000649)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (850)
Record Information
Version2.0
Creation Date2012-05-31 14:07:12 -0600
Update Date2015-09-17 15:41:57 -0600
Secondary Accession Numbers
  • ECMDB04169
Identification
Name:UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
DescriptionUDP-n-acetylmuramoyl-L-alanyl-D-glutamate is a member of the chemical class known as Peptides. These are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another. UDP-N-acetylmuramoyl-L-alanyl-D-glutamate is a key component of peptidoglycan synthesis. The peptidoglycan synthesis pathway starts at 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-alpha-D-glucosamine, yielding the complete monomeric unit a lipid , also known as lipid . This final lipid intermediate is transferred 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. UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-diaminopimelate ligase is a cytoplasmic enzyme that catalyzes the addition of meso-diaminopimelic acid to nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate in the biosynthesis of bacterial cell-wall peptidoglycan. (PMID 11124264)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • UDP-GlcNAcMurAlaGlu
  • UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate tetraanion
  • UDP-N-Acetylmuramoyl-L-alanyl-D-glutamic acid
  • UDP-N-Acetylmuramoyl-L-alanyl-D-glutamic acid tetraanion
  • Uridine 5'-(3-{2-acetamido-2-deoxy-3-O-[(2R)-1-{[(2S)-1-D-glutamato-1-oxopropan-2-yl]amino}-1-oxopropan-2-yl]-D-glucopyranosyl} diphosphate)
  • Uridine 5'-(3-{2-acetamido-2-deoxy-3-O-[(2R)-1-{[(2S)-1-D-glutamato-1-oxopropan-2-yl]amino}-1-oxopropan-2-yl]-D-glucopyranosyl} diphosphoric acid)
Chemical Formula:C22H32Cl2N2O4
Weight:Average: 459.41
Monoisotopic: 458.1739129
InChI Key:IEKOTSCYBBDIJC-UHFFFAOYSA-N
InChI:InChI=1S/C22H32Cl2N2O4/c1-3-5-7-13-26(14-8-6-4-2)22(30)19(11-12-20(27)28)25-21(29)16-9-10-17(23)18(24)15-16/h9-10,15,19H,3-8,11-14H2,1-2H3,(H,25,29)(H,27,28)
CAS number:17088-64-1
IUPAC Name:(2R)-2-({2-[(2-{[(3R,4R,5S,6R)-2-({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-4-yl]oxy}-1-hydroxypropylidene)amino]-1-hydroxypropylidene}amino)pentanedioic acid
Traditional IUPAC Name:(2R)-2-({2-[(2-{[(3R,4R,5S,6R)-2-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-4-yl]oxy}-1-hydroxypropylidene)amino]-1-hydroxypropylidene}amino)pentanedioic acid
SMILES:CCCCCN(CCCCC)C(=O)C(CCC(O)=O)N=C(O)C1=CC(Cl)=C(Cl)C=C1
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine nucleotide sugars
Direct ParentPyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine ribonucleoside diphosphate
  • Alpha-dipeptide
  • Alpha peptide
  • Pentose phosphate
  • Pentose-5-phosphate
  • N-acyl-alpha-hexosamine
  • Glutamic acid or derivatives
  • N-acyl-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid amide
  • Glycosyl compound
  • N-glycosyl compound
  • Alanine or derivatives
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Alpha-amino acid or derivatives
  • N-substituted-alpha-amino acid
  • Monoalkyl phosphate
  • Pyrimidone
  • Dicarboxylic acid or derivatives
  • Hydropyrimidine
  • Alkyl phosphate
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Acetamide
  • Secondary carboxylic acid amide
  • Urea
  • Lactam
  • Carboxamide group
  • Secondary alcohol
  • Dialkyl ether
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Ether
  • Oxacycle
  • Azacycle
  • Carboxylic acid
  • Primary alcohol
  • Alcohol
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Carbonyl group
  • Organonitrogen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Solid
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
LogP:-7.337PhysProp
Predicted Properties
PropertyValueSource
Water Solubility7.58 g/LALOGPS
logP-0.94ALOGPS
logP-3.2ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.72ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count24ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area436.17 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity180.16 m³·mol⁻¹ChemAxon
Polarizability76.89 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Diaminopimelic acid + Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate > ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanine + D-Glutamic acid <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Meso-2,6-Diaminoheptanedioate <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine + Adenosine triphosphate > Hydrogen ion + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Phosphate + ADP
<i>meso</i>-diaminopimelate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Adenosine triphosphate > Hydrogen ion + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + Phosphate + ADP
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanine + DL-Glutamic acid > ADP + Inorganic phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Meso-2,6-Diaminoheptanedioate > ADP + Inorganic phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine
UDP-N-Acetylmuramoyl-L-alanine + Adenosine triphosphate + D-Glutamic acid > Adenosine diphosphate + Phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + ADP + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + Meso-2,6-Diaminoheptanedioate + Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate > Adenosine diphosphate + Phosphate + Hydrogen ion + UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate + ADP
UDP-N-Acetylmuramyl-L-Ala + Adenosine triphosphate + D-Glutamic acid > UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + ADP + Phosphate
Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Meso-2,6-Diaminoheptanedioate <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Meso-2,6-Diaminoheptanedioate <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
SMPDB Pathways:
D-Glutamine and D-glutamate metabolismPW000769 ThumbThumb?image type=greyscaleThumb?image type=simple
Lysine biosynthesisPW000771 ThumbThumb?image type=greyscaleThumb?image type=simple
peptidoglycan biosynthesis IPW000906 ThumbThumb?image type=greyscaleThumb?image type=simple
peptidoglycan biosynthesis I 2PW002062 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-DAP-containing) PWY-6387
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0920000030-9501bc6942335865a32bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910000000-081da383d328cda7011bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3910000000-47d3cd7d61b410b044d3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-7902600380-4e6fc4dba489cd21009dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03ec-6914104040-1d9c3c55962ac034be03View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06tf-4923000000-36be71bdb3f634865e8dView in MoNA
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
  • van 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. Pubmed: 17765195
  • Winder, 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. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16970
HMDB IDNot Available
Pubchem Compound ID23724464
Kegg IDC00692
ChemSpider ID388428
Wikipedia IDNot Available
BioCyc IDUDP-AA-GLUTAMATE
EcoCyc IDUDP-AA-GLUTAMATE

Enzymes

Protein Details
1. UDP-N-acetylmuramoylalanine--D-glutamate ligase
General function:
Involved in ATP binding
Specific function:
Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA)
Gene Name:
murD
Uniprot ID:
P14900
Molecular weight:
46973
Reactions
ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.
Protein Details
2. UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
General function:
Involved in ATP binding
Specific function:
Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use many meso-diaminopimelate analogs as substrates, although much less efficiently, but not L-lysine
Gene Name:
murE
Uniprot ID:
P22188
Molecular weight:
53343
Reactions
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diamino-heptanedioate.