P. aeruginosa Metabolome Database: D-Glutamic acid (PAMDB000491)

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

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000491

Identification

Name:

D-Glutamic acid

Description:

D-glutamate 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. There are two forms of glutamic acid found in nature: L-glutamic acid and D-glutamic acid. D-glutamic acid is found naturally primarily in the cell walls of certain bacteria - including Pseudomonas aeruginosa. D-glutamate is also present in certain foods e.g., soybeans and also arises from the turnover of the intestinal tract microflora, whose cell walls contain significant D-glutamate. Unlike other D-amino acids, D-glutamate is not oxidized by the D-amino acid oxidases, and therefore this detoxification pathway is not available for handling D-glutamate. Likewise, D-glutamic acid, when ingested, largely escapes most deamination reactions (unlike the L-counterpart). D-glutamate is the most potent natural inhibitor of glutathione synthesis identified to date.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

(2R)-2-aminopentanedioate
(2R)-2-aminopentanedioic acid
(R)-2-aminopentanedioate
(R)-2-aminopentanedioic acid
D-2-Aminoglutarate
D-2-Aminoglutaric acid
D-2-Aminopentanedioate
D-2-Aminopentanedioic acid
D-Glu
D-Glutamate
D-Glutamic acid
D-Glutaminate
D-Glutaminic acid
D-Glutaminsaeure
Delta-2-Aminoglutarate
Delta-2-Aminoglutaric acid
Delta-2-Aminopentanedioate
Delta-2-Aminopentanedioic acid
Delta-Glutamate
Delta-Glutamic acid
Delta-Glutaminate
Delta-Glutaminic acid
Delta-Glutaminsaeure
DGL
Glutamate
Glutamate D-form
Glutamic acid
Glutamic acid D-form
Lopac-G-2128
Lopac-gamma-2128
Lopac-γ-2128
R-(-)-Glutamate
R-(-)-Glutamic acid
Tocris-0217
δ-2-Aminoglutarate
δ-2-Aminoglutaric acid
δ-2-Aminopentanedioate
δ-2-Aminopentanedioic acid
δ-Glutamate
δ-Glutamic acid
δ-Glutaminate
δ-Glutaminic acid
δ-Glutaminsaeure

Chemical Formula:

C₅H₉NO₄

Average Molecular Weight:

147.1293

Monoisotopic Molecular Weight:

147.053157781

InChI Key:

WHUUTDBJXJRKMK-GSVOUGTGSA-N

InChI:

InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1

CAS number:

6893-26-1

IUPAC Name:

(2R)-2-aminopentanedioic acid

Traditional IUPAC Name:

D-glutamic acid

SMILES:

N[C@H](CCC(O)=O)C(O)=O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Amino fatty acid
Fatty acyl
Fatty acid
Dicarboxylic acid or derivatives
Carboxylic 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

D-alpha-amino acid (CHEBI:15966 )
glutamic acid (CHEBI:15966 )
Other amino acids (C00217 )

Physical Properties

State:

Solid

Charge:

-1

Melting point:

201 °C

Experimental Properties:

Property	Value	Source
Water Solubility:	8.88 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	80.6 mg/mL	ALOGPS
logP	-3.5	ALOGPS
logP	-3.2	ChemAxon
logS	-0.26	ALOGPS
pKa (Strongest Acidic)	1.88	ChemAxon
pKa (Strongest Basic)	9.54	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	100.62 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.29 m³·mol^-1	ChemAxon
Polarizability	13.19 Å³	ChemAxon
Number of Rings	0	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:

Adenosine triphosphate + D-Glutamic acid + UDP-N-Acetylmuramoyl-L-alanine <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
D-Glutamic acid <> L-Glutamate
D-Glutamine + Water <> D-Glutamic acid + Ammonia
Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanine + D-Glutamic acid <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate
Pyridoxamine 5'-phosphate + Oxoglutaric acid <> Pyridoxal 5'-phosphate + D-Glutamic acid
L-Glutamic acid + L-Glutamate <> D-Glutamic acid
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

Pathways:

D-Glutamine and D-glutamate metabolism pae00471
Metabolic pathways pae01100
Peptidoglycan biosynthesis pae00550
Vitamin B6 metabolism pae00750

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-3900000000-58248bb2a0c7ddc905cf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0zgi-9600000000-076b628a6858a60a475f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-bd3823a5fab8a2d9b62c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-11233b5887638266e512	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fba-4900000000-1e8ea62e3fbd8467396f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0abc-9100000000-6c956e122b59de69a472	View in MoNA

References

References:

Ahlman B, Andersson K, Leijonmarck CE, Ljungqvist O, Hedenborg L, Wernerman J: Short-term starvation alters the free amino acid content of the human intestinal mucosa. Clin Sci (Lond). 1994 Jun;86(6):653-62. Pubmed: 7914846
Bill JR, Mack DG, Falta MT, Maier LA, Sullivan AK, Joslin FG, Martin AK, Freed BM, Kotzin BL, Fontenot AP: Beryllium presentation to CD4+ T cells is dependent on a single amino acid residue of the MHC class II beta-chain. J Immunol. 2005 Nov 15;175(10):7029-37. Pubmed: 16272364
Canal N, Nemni R: Autoimmunity and diabetic neuropathy. Clin Neurosci. 1997;4(6):371-3. Pubmed: 9358982
Cuervo JH, Rodriguez B, Houghten RA: The Magainins: sequence factors relevant to increased antimicrobial activity and decreased hemolytic activity. Pept Res. 1988 Nov-Dec;1(2):81-6. Pubmed: 2980783
Danke NA, Koelle DM, Yee C, Beheray S, Kwok WW: Autoreactive T cells in healthy individuals. J Immunol. 2004 May 15;172(10):5967-72. Pubmed: 15128778
Emi M, Wilson DE, Iverius PH, Wu L, Hata A, Hegele R, Williams RR, Lalouel JM: Missense mutation (Gly----Glu188) of human lipoprotein lipase imparting functional deficiency. J Biol Chem. 1990 Apr 5;265(10):5910-6. Pubmed: 1969408
Guariso G, Brotto F, Basso D, Alaggio R, Betterle C: Organ-specific autoantibodies in children with Helicobacter pylori infection. Helicobacter. 2004 Dec;9(6):622-8. Pubmed: 15610075
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
Luo J, Kaplitt MG, Fitzsimons HL, Zuzga DS, Liu Y, Oshinsky ML, During MJ: Subthalamic GAD gene therapy in a Parkinson's disease rat model. Science. 2002 Oct 11;298(5592):425-9. Pubmed: 12376704
Maechler P, Gjinovci A, Wollheim CB: Implication of glutamate in the kinetics of insulin secretion in rat and mouse perfused pancreas. Diabetes. 2002 Feb;51 Suppl 1:S99-102. Pubmed: 11815466
Majid SM, Liss AS, You M, Bose HR: The suppression of SH3BGRL is important for v-Rel-mediated transformation. Oncogene. 2006 Feb 2;25(5):756-68. Pubmed: 16186799
Mally MI, Cirulli V, Hayek A, Otonkoski T: ICA69 is expressed equally in the human endocrine and exocrine pancreas. Diabetologia. 1996 Apr;39(4):474-80. Pubmed: 8777998
Meyer W, Poehling HM, Neurand K: Intraepidermal distribution of free amino acids in porcine skin. J Dermatol Sci. 1991 Sep;2(5):383-92. Pubmed: 1742249
Nagai A, Suzuki Y, Baek SY, Lee KS, Lee MC, McLarnon JG, Kim SU: Generation and characterization of human hybrid neurons produced between embryonic CNS neurons and neuroblastoma cells. Neurobiol Dis. 2002 Oct;11(1):184-98. Pubmed: 12460557
Nielsen C, Hansen D, Husby S, Jacobsen BB, Lillevang ST: No allelic variation in genes with high gliadin homology in patients with celiac disease and type 1 diabetes. Immunogenetics. 2004 Aug;56(5):375-8. Epub 2004 Aug 7. Pubmed: 15309343
Persson H, Pelto-Huikko M, Metsis M, Soder O, Brene S, Skog S, Hokfelt T, Ritzen EM: Expression of the neurotransmitter-synthesizing enzyme glutamic acid decarboxylase in male germ cells. Mol Cell Biol. 1990 Sep;10(9):4701-11. Pubmed: 1697032
Raj D, Langford M, Krueger S, Shelton M, Welbourne T: Regulatory responses to an oral D-glutamate load: formation of D-pyrrolidone carboxylic acid in humans. Am J Physiol Endocrinol Metab. 2001 Feb;280(2):E214-20. Pubmed: 11158923
Roll U, Scheeser J, Standl E, Ziegler AG: Alterations of lymphocyte subsets in children of diabetic mothers. Diabetologia. 1994 Nov;37(11):1132-41. Pubmed: 7867885
Wang M, Meng Z, Fu J: Synthesis and biodistribution of six novel 99mTc complexes of 2-hydroxybenzaldehyde-amino acid Schiff bases. Appl Radiat Isot. 2006 Feb;64(2):235-40. Pubmed: 16309915
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:

Ozaki, Akio; Yagasaki, Makoto; Takada, Hideyoshi; Hashimoto, Yukio. Manufacture of D-glutamic acid with Lactobacillus. Jpn. Kokai Tokkyo Koho (1990), 4 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	15966
HMDB ID	HMDB03339
Pubchem Compound ID	23327
Kegg ID	C00217
ChemSpider ID	21814
Wikipedia	DGL
BioCyc ID	D-GLT
EcoCyc ID	D-GLT
Ligand Expo	FGA

Enzymes

Protein Details

• Glutaminase 2

General function:: Involved in glutaminase activity
Specific function:: L-glutamine + H(2)O = L-glutamate + NH(3)
Gene Name:: glsA2
Locus Tag:: PA1638
Molecular weight:: 33 kDa

Reactions

L-glutamine + H(2)O = L-glutamate + NH(3).

Protein Details

• 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
Locus Tag:: PA4414
Molecular weight:: 48.1 kDa

Reactions

ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.

Protein Details

• Glutamate racemase

General function:: Involved in racemase and epimerase activity, acting on amino acids and derivatives
Specific function:: Provides the (R)-glutamate required for cell wall biosynthesis
Gene Name:: murI
Locus Tag:: PA4662
Molecular weight:: 28.3 kDa

Reactions

L-glutamate = D-glutamate.

Protein Details

• Glutamate/aspartate transport system permease protein gltJ

General function:: Involved in transporter activity
Specific function:: Part of the binding-protein-dependent transport system for aspartate/glutamate; probably responsible for the translocation of the substrate across the membrane
Gene Name:: gltJ
Locus Tag:: PA1341
Molecular weight:: 27.6 kDa

Protein Details

• Glutamate/aspartate transport system permease protein gltK

General function:: Involved in transporter activity
Specific function:: Part of the binding-protein-dependent transport system for aspartate/glutamate; probably responsible for the translocation of the substrate across the membrane
Gene Name:: gltK
Locus Tag:: PA1340
Molecular weight:: 24.6 kDa

Transporters

Protein Details

• Uncharacterized amino-acid ABC transporter ATP-binding protein yecC

General function:: Involved in nucleotide binding
Specific function:: Probably part of a binding-protein-dependent transport system yecCS for an amino acid. Probably responsible for energy coupling to the transport system
Gene Name:: yecC
Locus Tag:: PA5152
Molecular weight:: 28.4 kDa

Protein Details

• Glutamate/aspartate transport system permease protein gltJ

General function:: Involved in transporter activity
Specific function:: Part of the binding-protein-dependent transport system for aspartate/glutamate; probably responsible for the translocation of the substrate across the membrane
Gene Name:: gltJ
Locus Tag:: PA1341
Molecular weight:: 27.6 kDa

Protein Details

• Glutamate/aspartate transport system permease protein gltK

General function:: Involved in transporter activity
Specific function:: Part of the binding-protein-dependent transport system for aspartate/glutamate; probably responsible for the translocation of the substrate across the membrane
Gene Name:: gltK
Locus Tag:: PA1340
Molecular weight:: 24.6 kDa

Protein Details

• Sodium/glutamate symport carrier protein

General function:: Involved in glutamate:sodium symporter activity
Specific function:: Catalyzes the sodium-dependent uptake of extracellular glutamate
Gene Name:: gltS
Locus Tag:: PA3176
Molecular weight:: 42.8 kDa

D-Glutamic acid (PAMDB000491)

Structure for D-Glutamic acid (PAMDB000491)

Enzymes

Reactions

Reactions

Reactions

Transporters