Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000504
Identification
Name: D-Alanyl-D-alanine
Description:D-Alanyl-D-alanine is a component of peptidoglycan. The ATP-dependent carboxylate-amine/thiol ligase superfamily is known to contain enzymes catalyzing the formation of various types of peptide, one of which is D-alanyl-D-alanine.
Structure
Thumb
Synonyms:
  • AlaAla
  • Alanyl-D-alanine
Chemical Formula: C6H12N2O3
Average Molecular Weight: 160.1711
Monoisotopic Molecular Weight: 160.08479226
InChI Key: DEFJQIDDEAULHB-QWWZWVQMSA-N
InChI:InChI=1S/C6H12N2O3/c1-3(7)5(9)8-4(2)6(10)11/h3-4H,7H2,1-2H3,(H,8,9)(H,10,11)/t3-,4-/m1/s1
CAS number: 923-16-0
IUPAC Name:(2R)-2-[(2R)-2-aminopropanamido]propanoic acid
Traditional IUPAC Name: D-ala-D-ala
SMILES:C[C@@H](N)C(=O)N[C@H](C)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds 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.
Kingdom Organic compounds
Super ClassOrganic acids and derivatives
Class Carboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct Parent Peptides
Alternative Parents
Substituents
  • Alpha peptide
  • N-acyl-aliphatic-alpha amino acid
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboximidic acid derivative
  • Carboximidic acid
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility70.7 mg/mLALOGPS
logP-2.6ALOGPS
logP-3.4ChemAxon
logS-0.36ALOGPS
pKa (Strongest Acidic)3.73ChemAxon
pKa (Strongest Basic)8.39ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area92.42 Å2ChemAxon
Rotatable Bond Count3ChemAxon
Refractivity37.79 m3·mol-1ChemAxon
Polarizability15.66 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Adenosine triphosphate + Water + D-Alanyl-D-alanine > ADP + D-Alanyl-D-alanine + Hydrogen ion + Phosphate
Adenosine triphosphate + Water + D-Alanyl-D-alanine > ADP + D-Alanyl-D-alanine + Hydrogen ion + Phosphate
two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain) > D-Alanyl-D-alanine + two disacharide linked murein units, pentapeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain)
2 D-Alanine + Adenosine triphosphate <> ADP + D-Alanyl-D-alanine + Hydrogen ion + Phosphate
D-Alanyl-D-alanine + Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate > ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine
D-Alanyl-D-alanine + Water >2 D-Alanine
Adenosine triphosphate + 2 D-Alanine <> ADP + Phosphate + D-Alanyl-D-alanine
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-Alanyl-D-alanine <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-Alanyl-D-alanine <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine
Adenosine triphosphate + 2 D-Alanine > ADP + Inorganic phosphate + D-Alanyl-D-alanine
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-Alanyl-D-alanine > ADP + Inorganic phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine
2 D-Alanine + Adenosine triphosphate > D-Alanyl-D-alanine + Adenosine diphosphate + Phosphate + ADP
UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate + D-Alanyl-D-alanine + Adenosine triphosphate > Adenosine diphosphate + Phosphate + Hydrogen ion + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ADP
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0296-5900000000-799966b5c9620715d16aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-9200000000-513a3e368e7c6334e54fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-006x-9000000000-0724d314ee5219f1c728View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-2900000000-b6d1f12edd1486d8cbb4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-059i-9600000000-8635adeca87ba2d6a666View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00du-9000000000-17647b2edc99cfa2d13bView in MoNA
References
References:
  • Franken N, Seidl PH, Kuchenbauer T, Kolb HJ, Schleifer KH, Weiss L, Tympner KD: Specific immunoglobulin A antibodies to a peptide subunit sequence of bacterial cell wall peptidoglycan. Infect Immun. 1984 Apr;44(1):182-7. Pubmed: 6423541
  • Jansen A, Turck M, Szekat C, Nagel M, Clever I, Bierbaum G: Role of insertion elements and yycFG in the development of decreased susceptibility to vancomycin in Staphylococcus aureus. Int J Med Microbiol. 2007 Jul;297(4):205-15. Epub 2007 Apr 5. Pubmed: 17418637
  • 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
  • Kovac A, Majce V, Lenarsic R, Bombek S, Bostock JM, Chopra I, Polanc S, Gobec S: Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl). Bioorg Med Chem Lett. 2007 Apr 1;17(7):2047-54. Epub 2007 Jan 17. Pubmed: 17267218
  • Ladesic B, Tomasic J, Kveder S, Hrsak I: The metabolic fate of 14C-labeled immunoadjuvant peptidoglycan monomer. II. In vitro studies. Biochim Biophys Acta. 1981 Nov 18;678(1):12-7. Pubmed: 6118181
  • Tabata, K., Ikeda, H., Hashimoto, S. (2005). "ywfE in Bacillus subtilis codes for a novel enzyme, L-amino acid ligase." J Bacteriol 187:5195-5202. Pubmed: 16030213
  • 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: Neuhaus, Francis C. Enzymic synthesis of D-alanyl-D-alanine. Biochemical and Biophysical Research Communications (1960), 3 401-5.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID16576
HMDB IDHMDB03459
Pubchem Compound ID5460362
Kegg IDC00993
ChemSpider ID4573916
Wikipedia IDNot Available
BioCyc IDD-ALA-D-ALA
EcoCyc IDD-ALA-D-ALA

Enzymes

General function:
Involved in catalytic activity
Specific function:
Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits)
Gene Name:
mrcB
Locus Tag:
PA4700
Molecular weight:
85.5 kDa
Reactions
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
General function:
Involved in ATP binding
Specific function:
Cell wall formation
Gene Name:
ddlB
Locus Tag:
PA4410
Molecular weight:
34.4 kDa
Reactions
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
General function:
Involved in ATP binding
Specific function:
Cell wall formation
Gene Name:
ddlA
Locus Tag:
PA4201
Molecular weight:
36.5 kDa
Reactions
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
General function:
Involved in ATP binding
Specific function:
Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein
Gene Name:
murF
Locus Tag:
PA4416
Molecular weight:
47.4 kDa
Reactions
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine.
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for dipeptides; probably responsible for the translocation of the substrate across the membrane
Gene Name:
dppB
Locus Tag:
PA4503
Molecular weight:
37 kDa
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for dipeptides; probably responsible for the translocation of the substrate across the membrane
Gene Name:
dppC
Locus Tag:
PA4504
Molecular weight:
32.4 kDa
General function:
Involved in nucleotide binding
Specific function:
Part of the binding-protein-dependent transport system for dipeptides. Probably responsible for energy coupling to the transport system
Gene Name:
dppD
Locus Tag:
PA4505
Molecular weight:
35.4 kDa
General function:
Involved in nucleotide binding
Specific function:
Part of the binding-protein-dependent transport system for dipeptides. Probably responsible for energy coupling to the transport system
Gene Name:
dppF
Locus Tag:
PA4506
Molecular weight:
36.3 kDa
General function:
Involved in transporter activity
Specific function:
Dipeptide-binding protein of a transport system that can be subject to osmotic shock. DppA is also required for peptide chemotaxis
Gene Name:
dppA
Locus Tag:
PA4496
Molecular weight:
60.1 kDa

Transporters

General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for dipeptides; probably responsible for the translocation of the substrate across the membrane
Gene Name:
dppB
Locus Tag:
PA4503
Molecular weight:
37 kDa
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for dipeptides; probably responsible for the translocation of the substrate across the membrane
Gene Name:
dppC
Locus Tag:
PA4504
Molecular weight:
32.4 kDa
General function:
Involved in nucleotide binding
Specific function:
Part of the binding-protein-dependent transport system for dipeptides. Probably responsible for energy coupling to the transport system
Gene Name:
dppD
Locus Tag:
PA4505
Molecular weight:
35.4 kDa
General function:
Involved in nucleotide binding
Specific function:
Part of the binding-protein-dependent transport system for dipeptides. Probably responsible for energy coupling to the transport system
Gene Name:
dppF
Locus Tag:
PA4506
Molecular weight:
36.3 kDa
General function:
Involved in transporter activity
Specific function:
Dipeptide-binding protein of a transport system that can be subject to osmotic shock. DppA is also required for peptide chemotaxis
Gene Name:
dppA
Locus Tag:
PA4496
Molecular weight:
60.1 kDa