P. aeruginosa Metabolome Database: L-Ala-gamma-D-Glu-Dap (PAMDB001378)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB001378

Identification

Name:

L-Ala-gamma-D-Glu-Dap

Description:

L-ala-gamma-D-glu-DAP is a member of the chemical class known as Hybrid Peptides. These are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta). L-alanyl-gamma-D-glutamyl-meso-diaminopimelate is related to MppA. MppA is a periplasmic binding protein in Pseudomonas aeruginosa essential for uptake of the cell wall murein tripeptide L-alanyl-gamma-D-glutamyl-meso-diaminopimelate. (PMID 10438753)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

L-Ala-γ-D-Glu-diaminopimelate
L-Ala-γ-D-glu-diaminopimelic acid
L-Ala-g-D-glu-dap
L-Ala-g-D-glu-diaminopimelate
L-Ala-g-D-glu-diaminopimelic acid
L-Ala-gamma-D-Glu-diaminopimelate
L-Ala-gamma-D-Glu-diaminopimelic acid
L-Ala-γ-D-glu-dap
L-Ala-γ-D-glu-diaminopimelate
L-Ala-γ-D-glu-diaminopimelic acid
L-alanyl-γ-D-glutamyl-meso-diaminopimelate
L-Alanyl-γ-D-glutamyl-meso-diaminopimelate
L-Alanyl-γ-D-glutamyl-meso-diaminopimelic acid
L-Alanyl-g-D-glutamyl-meso-diaminopimelate
L-Alanyl-g-D-glutamyl-meso-diaminopimelic acid
L-Alanyl-gamma-D-glutamyl-meso-diaminopimelate
L-Alanyl-gamma-D-glutamyl-meso-diaminopimelic acid
L-Alanyl-γ-D-glutamyl-meso-diaminopimelate
L-Alanyl-γ-D-glutamyl-meso-diaminopimelic acid

Chemical Formula:

C₁₃H₁₉N₅O₄

Average Molecular Weight:

309.3211

Monoisotopic Molecular Weight:

309.143704121

InChI Key:

IBYVCSBRMYGDRR-UHFFFAOYSA-N

InChI:

InChI=1S/C13H19N5O4/c1-7(14)12(21)16-8(5-6-11(19)20)13(22)18-10-4-2-3-9(15)17-10/h2-4,7-8H,5-6,14H2,1H3,(H,16,21)(H,19,20)(H3,15,17,18,22)

CAS number:

Not Available

IUPAC Name:

4-[(2-amino-1-hydroxypropylidene)amino]-4-[(6-imino-1,6-dihydropyridin-2-yl)-C-hydroxycarbonimidoyl]butanoic acid

Traditional IUPAC Name:

4-[(2-amino-1-hydroxypropylidene)amino]-4-[(6-imino-1H-pyridin-2-yl)-C-hydroxycarbonimidoyl]butanoic acid

SMILES:

CC(N)C(O)=NC(CCC(O)=O)C(O)=NC1=CC=CC(=N)N1

Chemical Taxonomy

Taxonomy Description

This 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 Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Peptides

Alternative Parents

Substituents

Alpha peptide
Dihydropyridine
Aminopyridine
Imidolactam
Pyridine
Hydropyridine
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
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
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.134 mg/mL	ALOGPS
logP	-2.3	ALOGPS
logP	-4.3	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	-0.17	ChemAxon
pKa (Strongest Basic)	18.93	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	164.38 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	99.88 m³·mol^-1	ChemAxon
Polarizability	31.29 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

L-Ala-gamma-D-Glu-Dap + Water > L-Ala-gamma-D-Glu + <i>meso</i>-diaminopimelate

Pathways:

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ox-2291000000-38d20bfeccd6193a9667	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-9640000000-e36d23ec2ab250ad0907	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udl-5900000000-365ab7bec0844109a8eb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-2479000000-239a5ac85243fd7da0ae	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0abc-5591000000-d77de6753708b9b588b6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9510000000-1de09e609196b35af68f	View in MoNA

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
Li, H., Park, J. T. (1999). "The periplasmic murein peptide-binding protein MppA is a negative regulator of multiple antibiotic resistance in Escherichia coli." J Bacteriol 181:4842-4847. Pubmed: 10438753
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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	656477
Kegg ID	Not Available
ChemSpider ID	570864
Wikipedia ID	Not Available
BioCyc ID	L-ALA-GAMMA-D-GLU-DAP
EcoCyc ID	L-ALA-GAMMA-D-GLU-DAP

Enzymes

Protein Details

• 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
Locus Tag:: PA1818
Molecular weight:: 82.8 kDa

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.

L-Ala-gamma-D-Glu-Dap (PAMDB001378)

Structure for L-Ala-gamma-D-Glu-Dap (PAMDB001378)

Enzymes

Reactions