UDP-N-Acetylmuramoyl-L-alanine (ECMDB04168) (M2MDB000648)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (828)
Record Information
Version2.0
Creation Date2012-05-31 14:07:09 -0600
Update Date2015-06-03 15:54:49 -0600
Secondary Accession Numbers
  • ECMDB04168
Identification
Name:UDP-N-Acetylmuramoyl-L-alanine
DescriptionUdp-n-acetylmuramoyl-l-alanine belongs to the class of Pyrimidine Nucleotide Sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. (inferred from compound structure)UDP-N-acetylmuramoyl-L-alanine (UDP-MurNAc-L-Ala), which is the nucleotide substrate of the D-glutamic-acid-adding enzyme (the murD gene product) catalyzing the subsequent step in the pathway for peptidoglycan synthesis, appears to be an effector of the racemase activity. (PMID 8098327) MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase) is the second enzyme in the series of Mur ligases, and it catalyzes the addition of D-glutamic acid (D-Glu) to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA). (PMID 19007109)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • UDP-N-acetylmuramoyl-L-alanine
  • UDP-MurNAcAla
Chemical Formula:C23H36N4O20P2
Weight:Average: 750.4943
Monoisotopic: 750.139812636
InChI Key:NTMMCWJNQNKACG-CPDMUANVSA-N
InChI:InChI=1S/C23H36N4O20P2/c1-8(21(35)36)24-19(34)9(2)43-18-14(25-10(3)29)22(45-11(6-28)16(18)32)46-49(40,41)47-48(38,39)42-7-12-15(31)17(33)20(44-12)27-5-4-13(30)26-23(27)37/h4-5,8-9,11-12,14-18,20,22,28,31-33H,6-7H2,1-3H3,(H,24,34)(H,25,29)(H,35,36)(H,38,39)(H,40,41)(H,26,30,37)/t8-,9+,11+,12+,14+,15+,16+,17+,18+,20+,22?/m0/s1
CAS number:78738-65-5
IUPAC Name:(2S)-2-{[(2R)-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}propanoic acid
Traditional IUPAC Name:(2S)-2-{[(2R)-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}propanoic acid
SMILES:[H][C@](C)(O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO)OC([H])(OP(O)(=O)OP(O)(=O)OC[C@@]2([H])O[C@@]([H])(N3C=CC(O)=NC3=O)[C@]([H])(O)[C@]2([H])O)[C@]1([H])N=C(C)O)C(O)=N[C@@]([H])(C)C(O)=O
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
  • Pentose phosphate
  • Pentose-5-phosphate
  • N-acyl-alpha-hexosamine
  • N-acyl-alpha-amino acid
  • N-acyl-l-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • Alanine or derivatives
  • Alpha-amino acid or derivatives
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Hydropyrimidine
  • Oxane
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Vinylogous amide
  • Acetamide
  • Heteroaromatic compound
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Urea
  • Carboxamide group
  • Lactam
  • Carboxylic acid derivative
  • Carboxylic acid
  • Dialkyl ether
  • Ether
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Oxacycle
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Primary alcohol
  • Organooxygen compound
  • Organic nitrogen compound
  • Organic oxide
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
LogP:-6.528PhysProp
Predicted Properties
PropertyValueSource
Water Solubility17.3 g/LALOGPS
logP-1.3ALOGPS
logP-3.1ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area366.28 ŲChemAxon
Rotatable Bond Count15ChemAxon
Refractivity151.55 m³·mol⁻¹ChemAxon
Polarizability64.63 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
L-Alanine + Adenosine triphosphate + UDP-N-Acetylmuraminate <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanine
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanine + D-Glutamic acid <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Adenosine triphosphate + UDP-N-Acetylmuraminate + L-Alanine <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanine
D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine + Adenosine triphosphate > Hydrogen ion + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate + Phosphate + ADP
Adenosine triphosphate + UDP-N-Acetylmuraminate + L-Alanine > ADP + Inorganic phosphate + UDP-N-Acetylmuramoyl-L-alanine
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanine + DL-Glutamic acid > ADP + Inorganic phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
UDP-N-acetylmuraminate + Adenosine triphosphate + L-Alanine + UDP-N-Acetylmuraminate + L-Alanine > UDP-N-Acetylmuramoyl-L-alanine + Adenosine diphosphate + Phosphate + ADP
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-acetyl-α-D-muramate + L-Alanine + Adenosine triphosphate + L-Alanine > Adenosine diphosphate + Phosphate + Hydrogen ion + UDP-N-Acetylmuramoyl-L-alanine + ADP
L-Alanine + Adenosine triphosphate + UDP-N-Acetylmuraminate <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanine
Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
L-Alanine + Adenosine triphosphate + UDP-N-Acetylmuraminate <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanine
Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
SMPDB Pathways:
D-Glutamine and D-glutamate metabolismPW000769 ThumbThumb?image type=greyscaleThumb?image type=simple
peptidoglycan biosynthesis IPW000906 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 GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-5900000200-10c08e7fa5be20ae1807View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-c709a71b4651bce45ce7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03du-9400000000-c0d9160051e7f7f2b7a0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-8914303600-11b64513dcd6d6c45ba1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-08gl-9713130300-9485d5c1d45c8be86f5bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06tf-5912000000-6bffb4709eadd4c8f246View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Humljan, J., Kotnik, M., Contreras-Martel, C., Blanot, D., Urleb, U., Dessen, A., Solmajer, T., Gobec, S. (2008). "Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme." J Med Chem 51:7486-7494. Pubmed: 19007109
  • 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 ID16932
HMDB IDNot Available
Pubchem Compound ID23724467
Kegg IDC01212
ChemSpider ID388547
Wikipedia IDNot Available
BioCyc IDCPD0-1456
EcoCyc IDCPD0-1456

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-acetylmuramate--L-alanine ligase
General function:
Involved in ATP binding
Specific function:
Cell wall formation
Gene Name:
murC
Uniprot ID:
P17952
Molecular weight:
53626
Reactions
ATP + UDP-N-acetylmuramate + L-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanine.