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UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine (M2MDB001419)

Record Information
Version2.0
Creation Date2012-05-31 14:53:51 -0600
Update Date2015-06-03 17:20:24 -0600
Secondary Accession Numbers
  • ECMDB20621
Identification
Name:UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine
DescriptionUDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine 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. It 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.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • UDP-N-acetylmuramoyl-L-alanyl-D-γ-Glu-6-carboxy-L-lys-D-ala
  • UDP-N-acetylmuramoyl-L-alanyl-D-γ-glutamyl-6-carboxy-L-lysl-D-alaniine
  • UDP-N-acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelyl-D-alanine
  • UDP-Murnac-tetrapeptide
  • UDP-n-Acetylmuramoyl-L-alanyl-D-γ-glu-6-carboxy-L-lys-D-ala
  • UDP-n-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-6-carboxy-L-lysl-D-alaniine
  • UDP-n-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelyl-D-alanine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-g-glu-6-carboxy-L-lys-D-ala
  • UDP-N-Acetylmuramoyl-L-alanyl-D-g-glutamyl-6-carboxy-L-lysl-D-alaniine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-g-glutamyl-meso-2,6-diaminopimelyl-D-alanine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-Glu-6-carboxy-L-lys-D-ala
  • UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-6-carboxy-L-lysl-D-alaniine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelyl-D-alanine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioic acid-D-alanine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glu-6-carboxy-L-lys-D-ala
  • UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-6-carboxy-L-lysl-D-alaniine
  • UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelyl-D-alanine
  • Uridine 5'-pyrophosphoryl N-acetylmuramyl-tetrapeptide
  • Uridine 5'-pyrophosphoryl N-acetylmuramyl-tetrapeptide
Chemical Formula:C38H56N8O27P2
Weight:Average: 1118.8362
Monoisotopic: 1118.27301165
InChI Key:UHRGSQREVOYTOH-HOZNVNQUSA-L
InChI:InChI=1S/C38H58N8O27P2/c1-14(30(54)44-20(36(61)62)8-9-23(49)43-19(7-5-6-18(39)35(59)60)32(56)41-15(2)34(57)58)40-31(55)16(3)69-29-25(42-17(4)48)37(71-21(12-47)27(29)52)72-75(66,67)73-74(64,65)68-13-22-26(51)28(53)33(70-22)46-11-10-24(50)45-38(46)63/h10-11,14-16,18-22,25-29,33,37,47,51-53H,5-9,12-13,39H2,1-4H3,(H9-2,40,41,42,43,44,45,48,49,50,54,55,56,57,58,59,60,61,62,63,64,65,66,67)/p-2/t14-,15+,16+,18+,19-,20+,21+,22+,25+,26+,27+,28+,29+,33+,37+/m0/s1
CAS number:Not Available
IUPAC Name:1-[(2R,3R,4S,5R)-5-{[({[(2R,3R,4R,5S,6R)-4-[(1R)-1-{[(1S)-1-{[(1R)-3-{[(1S,5R)-5-amino-5-carboxy-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}pentyl]carboximidato}-1-carboxypropyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}ethoxy]-5-hydroxy-6-(hydroxymethyl)-3-[(1-oxidoethylidene)amino]oxan-2-yl phosphonato]oxy}phosphinato)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-2-oxo-2,5-dihydro-1λ⁵-pyrimidine-1,5-bis(ylium)
Traditional IUPAC Name:1-[(2R,3R,4S,5R)-5-[({[(2R,3R,4R,5S,6R)-4-[(1R)-1-{[(1S)-1-{[(1R)-3-{[(1S,5R)-5-amino-5-carboxy-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}pentyl]carboximidato}-1-carboxypropyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}ethoxy]-5-hydroxy-6-(hydroxymethyl)-3-[(1-oxidoethylidene)amino]oxan-2-yl phosphonato]oxyphosphinato}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-2-oxo-5H-1λ⁵-pyrimidine-1,5-bis(ylium)
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)OC[C@@]2([H])O[C@@]([H])([N+]3=C[CH+]C(O)=NC3=O)[C@]([H])(O)[C@]2([H])O)[C@]1([H])N=C(C)[O-])C(O)=O)C(O)=N[C@]([H])(C)C(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as peptides. Peptides 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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentPeptides
Alternative Parents
Substituents
  • Alpha peptide
  • Pentose-5-phosphate
  • Pentose phosphate
  • N-acyl-alpha-hexosamine
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Alanine or derivatives
  • N-glycosyl compound
  • Glycosyl compound
  • D-alpha-amino acid
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Monosaccharide
  • 2,5-dihydropyrimidine
  • Hydropyrimidine
  • Tetrahydrofuran
  • Amino acid
  • Secondary alcohol
  • Carbonic acid derivative
  • Amino acid or derivatives
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.56 g/LALOGPS
logP0.67ALOGPS
logP-6.1ChemAxon
logS-3.4ALOGPS
pKa (Strongest Acidic)-6.9ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count31ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area575.76 ŲChemAxon
Rotatable Bond Count29ChemAxon
Refractivity256.48 m³·mol⁻¹ChemAxon
Polarizability101.01 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine + Water > L-Alanine + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-1900000000-b7918bdd8b3ff79a276aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3900000000-7a3e89d0eccd31473096View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-4900000000-1720dcb46c7116174653View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0170-6900000000-791a708b0c9f9836e7bfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9300000000-58fe4a3788c60b9b23c8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9200000000-9d1bea0563cfe0744e69View 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:
  • 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 IDNot Available
HMDB IDNot Available
Pubchem Compound ID25200511
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDUDP-MURNAC-TETRAPEPTIDE
EcoCyc IDUDP-MURNAC-TETRAPEPTIDE

Enzymes

Protein Details
1. Murein tetrapeptide carboxypeptidase
General function:
Defense mechanisms
Specific function:
Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso- Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc- anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross- linked muropeptides. The tripeptides produced by the lcdA reaction can then be reused as peptidoglycan building blocks; lcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase
Gene Name:
ldcA
Uniprot ID:
P76008
Molecular weight:
33567
Reactions
GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H(2)O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine.