Diaminopimelic acid (PAMDB000360)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000360
Identification
Name: Diaminopimelic acid
Description:Diaminopimelic acid (DAP) is an amino acid, representing an epsilon-carboxy derivative of lysine. DAP found in the cell walls of Pseudomonas aeruginosa and is a component of peptidoglycan of Gram-negative bacteria.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • ( (R*,S*)-2,6-diamino-Heptanedioate
  • ( (R*,S*)-2,6-diamino-Heptanedioic acid
  • (2R,6S)-2,6-diamino-heptanedioate
  • (2R,6S)-2,6-diamino-heptanedioic acid
  • (R*,S*)-2,6-diamino-Heptanedioate
  • (R*,S*)-2,6-diamino-Heptanedioic acid
  • 2,6-Diamino-Heptanedioate
  • 2,6-Diamino-Heptanedioic acid
  • 2,6-Diaminoheptanedioate
  • 2,6-Diaminoheptanedioic acid
  • 2,6-Diaminopimelate
  • 2,6-Diaminopimelic acid
  • A,a'-Diaminopimelate
  • A,a'-Diaminopimelic acid
  • A,e-Diaminopimelate
  • A,e-Diaminopimelic acid
  • D,L-Diaminopimelate
  • D,L-Diaminopimelic acid
  • D,L-Meso-diaminoheptanedioate
  • D,L-Meso-diaminoheptanedioic acid
  • DAPA
  • Diaminopimelate
  • Diaminopimelic acid
  • Dl-2,6-Diaminoheptanedioate
  • Dl-2,6-Diaminoheptanedioic acid
  • DL-2,6-Diaminopimelate
  • DL-2,6-Diaminopimelic acid
  • DPA
  • L,L-2,6-Diaminoheptanedioate
  • L,L-2,6-Diaminoheptanedioic acid
  • L,L-2,6-Diaminopimelate
  • L,L-2,6-Diaminopimelic acid
  • L,L-A2pm
  • L,L-DAP
  • L,L-Diaminopimelate
  • L,L-Diaminopimelic acid
  • LL-2,6-diaminoheptanedioate
  • LL-2,6-diaminoheptanedioic acid
  • LL-2,6-Diaminopimelate
  • LL-2,6-Diaminopimelic acid
  • meso-1-a,epsilon-Diaminopimelate
  • meso-1-a,epsilon-Diaminopimelic acid
  • Meso-1-alpha,epsilon-diaminopimelate
  • Meso-1-alpha,epsilon-diaminopimelic acid
  • meso-1-α,epsilon-Diaminopimelate
  • meso-1-α,epsilon-Diaminopimelic acid
  • Meso-2,6-diamino-Heptanedioate
  • Meso-2,6-diamino-Heptanedioic acid
  • Meso-2,6-diaminoheptanedioate
  • Meso-2,6-diaminoheptanedioic acid
  • meso-a,Alpha'-diaminopimelate
  • meso-a,Alpha'-diaminopimelic acid
  • meso-a,epsilon-Diaminopimelate
  • meso-a,epsilon-Diaminopimelic acid
  • Meso-alpha,alpha'-Diaminopimelate
  • Meso-alpha,alpha'-Diaminopimelic acid
  • Meso-alpha,epsilon-Diaminopimelate
  • Meso-alpha,epsilon-Diaminopimelic acid
  • Meso-diaminoheptanedioate
  • Meso-diaminoheptanedioic acid
  • Meso-diaminopimelate
  • Meso-diaminopimelic acid
  • meso-α,Alpha'-diaminopimelate
  • meso-α,Alpha'-diaminopimelic acid
  • meso-α,epsilon-Diaminopimelate
  • meso-α,epsilon-Diaminopimelic acid
Chemical Formula: C7H14N2O4
Average Molecular Weight: 190.1971
Monoisotopic Molecular Weight: 190.095356946
InChI Key: GMKMEZVLHJARHF-WHFBIAKZSA-N
InChI:InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1
CAS number: 583-93-7
IUPAC Name:(2S,6S)-2,6-diaminoheptanedioic acid
Traditional IUPAC Name: diamino-pimelic acid
SMILES:N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
Kingdom Organic compounds
Super ClassOrganic acids and derivatives
Class Carboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct Parent L-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Medium-chain fatty 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
Physical Properties
State: Solid
Charge:0
Melting point: 300 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility14.1 mg/mLALOGPS
logP-4.1ALOGPS
logP-5.5ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)9.83ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area126.64 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity43.64 m3·mol-1ChemAxon
Polarizability18.93 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Diaminopimelic acid + Adenosine triphosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate > ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate + Water > Diaminopimelic acid + L-Alanyl-D-glutamate
Water + N-Succinyl-L,L-2,6-diaminopimelate <> Diaminopimelic acid + Succinic acid
Diaminopimelic acid + Hydrogen ion > Carbon dioxide + L-Lysine
Diaminopimelic acid <> Meso-2,6-Diaminoheptanedioate
Diaminopimelic acid <> <i>meso</i>-diaminopimelate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0umi-1950000000-749403a0eb6d05c7903eView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0uk9-1980000000-1b092f9141e7549bee24View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004l-0900000000-d85213bd7ac426f10cd7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9100000000-add590f1b216bdb40334View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-de98ed3bb8c48b6f9852View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Borruat G, Roten CA, Fay LB, Karamata D: A high-performance liquid chromatography method for the detection of diaminopimelic acid in urine. Anal Biochem. 2001 Apr 1;291(1):11-6. Pubmed: 11262151
  • Hamaker BR, Rivera K, Morales E, Graham GG: Effect of dietary fiber and starch on fecal composition in preschool children consuming maize, amaranth, or cassava flours. J Pediatr Gastroenterol Nutr. 1991 Jul;13(1):59-66. Pubmed: 1656007
  • Iida S, Taniguchi H, Kageyama A, Yazawa K, Chibana H, Murata S, Nomura F, Kroppenstedt RM, Mikami Y: Gordonia otitidis sp. nov., isolated from a patient with external otitis. Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1871-6. Pubmed: 16166681
  • 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
  • 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
  • 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: Gao, Yong. Synthesis of diaminopimelic acid (DAP) and analogues: mechanistic studies on DAP aminotransferase, epimerase and dehydrogenase. (1998), 166 pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID23673
HMDB IDHMDB01370
Pubchem Compound ID865
Kegg IDC00666
ChemSpider ID388416
Wikipedia IDNot Available
BioCyc IDLL-DIAMINOPIMELATE
EcoCyc IDLL-DIAMINOPIMELATE

Enzymes

Protein Details
• Diaminopimelate decarboxylase
General function:
Involved in catalytic activity
Specific function:
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2)
Gene Name:
lysA
Locus Tag:
PA5277
Molecular weight:
45.5 kDa
Reactions
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2).
Protein Details
• Diaminopimelate epimerase
General function:
Involved in diaminopimelate epimerase activity
Specific function:
LL-2,6-diaminoheptanedioate = meso- diaminoheptanedioate
Gene Name:
dapF
Locus Tag:
PA5278
Molecular weight:
30.3 kDa
Reactions
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.
Protein Details
• Succinyl-diaminopimelate desuccinylase
General function:
Involved in metallopeptidase activity
Specific function:
Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
Gene Name:
dapE
Locus Tag:
PA1162
Molecular weight:
41.1 kDa
Reactions
N-succinyl-LL-2,6-diaminoheptanedioate + H(2)O = succinate + LL-2,6-diaminoheptanedioate.
Protein Details
• UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
General function:
Involved in ATP binding
Specific function:
Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use many meso-diaminopimelate analogs as substrates, although much less efficiently, but not L-lysine
Gene Name:
murE
Locus Tag:
PA4417
Molecular weight:
51.3 kDa
Reactions
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diamino-heptanedioate.

Transporters

Protein Details
• Diaminopimelate epimerase
General function:
Involved in diaminopimelate epimerase activity
Specific function:
LL-2,6-diaminoheptanedioate = meso- diaminoheptanedioate
Gene Name:
dapF
Locus Tag:
PA5278
Molecular weight:
30.3 kDa
Reactions
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.