GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine (ECMDB23146) (M2MDB003536)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-10-10 12:18:51 -0600
Update Date2015-06-03 17:26:01 -0600
Secondary Accession Numbers
  • ECMDB23146
Identification
Name:GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine
DescriptionGlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine is an intermediate in peptidoglycan recylcing and biosynthesis. It is a substrate for the enzyme Murein tetrapeptide carboxypeptidase (lcdA) which releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. The tripeptides produced by the lcdA reaction can then be reused as peptidoglycan building blocks.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • GlcNAc-murnac-L-alanyl-g-D-glutamyl-meso-diaminopimelyl-D-alanine
  • GlcNAc-murnac-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanine
Chemical Formula:C34H57N7O19
Weight:Average: 867.8519
Monoisotopic: 867.370922677
InChI Key:MKQQKXDNMLOSJC-YFCMHDTQSA-N
InChI:InChI=1S/C34H57N7O19/c1-12(28(51)40-18(8-9-21(46)47)30(53)41-17(7-5-6-16(35)33(56)57)29(52)36-13(2)32(54)55)37-31-22(38-14(3)44)26(50)27(20(11-43)58-31)60-34-23(39-15(4)45)25(49)24(48)19(10-42)59-34/h12-13,16-20,22-27,31,34,37,42-43,48-50H,5-11,35H2,1-4H3,(H,36,52)(H,38,44)(H,39,45)(H,40,51)(H,41,53)(H,46,47)(H,54,55)(H,56,57)/t12-,13+,16-,17+,18+,19+,20+,22+,23+,24+,25+,26+,27+,31+,34-/m0/s1
CAS number:Not Available
IUPAC Name:(2S,6R)-2-amino-6-{[(2R)-4-carboxy-2-{[(2S)-2-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]amino}-1-hydroxypropylidene]amino}-1-hydroxybutylidene]amino}-6-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}hexanoic acid
Traditional IUPAC Name:(2S,6R)-2-amino-6-{[(2R)-4-carboxy-2-{[(2S)-2-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]amino}-1-hydroxypropylidene]amino}-1-hydroxybutylidene]amino}-6-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}hexanoic acid
SMILES:[H][C@](N)(CCC[C@@]([H])(N=C(O)[C@@]([H])(CCC(O)=O)N=C(O)[C@]([H])(C)N[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O[C@]2([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])N=C(C)O)[C@]([H])(O)[C@@]1([H])N=C(C)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
  • N-acyl-alpha-hexosamine
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Alanine or derivatives
  • O-glycosyl compound
  • N-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • L-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Oxane
  • Amino acid
  • Secondary alcohol
  • Hemiaminal
  • Amino acid or derivatives
  • Oxacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Secondary amine
  • Secondary aliphatic amine
  • Carboxylic acid
  • Carboximidic acid derivative
  • Carboximidic acid
  • Acetal
  • 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
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.15 g/LALOGPS
logP-2ALOGPS
logP-3.2ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)3.31ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count26ChemAxon
Hydrogen Donor Count15ChemAxon
Polar Surface Area441.74 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity195.98 m³·mol⁻¹ChemAxon
Polarizability84.28 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + Water > GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-Alanine
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, Positivesplash10-0udi-0010100190-9e8437f30e77ca82288dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udl-8173913260-67cfd8fb9e4f7b1e366fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udl-9680720150-1f0385d690fa183cec14View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-05p2-3100113890-92d62d11895cdca78711View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0005-1020390020-2d013bb94070609a61d2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0r09-9224233000-16c8934fc82e31b99d3dView in MoNA
MSMass Spectrum (Electron Ionization)Not 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
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

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.