ECMDB: Diaminopimelic acid (ECMDB01370) (M2MDB000360)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (5)Transporters (5)XML

Proteins (938)

Record Information

Version

2.0

Creation Date

2012-05-31 13:51:08 -0600

Update Date

2015-09-13 12:56:11 -0600

Secondary Accession Numbers

ECMDB01370

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 E. coli and is a component of peptidoglycan of Gram-negative bacteria.

Structure

MOL SDF PDB SMILES InChI

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

Weight:

Average: 190.1971
Monoisotopic: 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

Description

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 Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Medium-chain fatty acid
Amino fatty acid
Dicarboxylic acid or derivatives
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Organopnictogen compound
Organic nitrogen compound
Amine
Organic oxygen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,6-diaminopimelic acid (CHEBI:16026 )
Dicarboxylic acids (LMFA01170102 )

Physical Properties

State:

Solid

Charge:

Melting point:

300 °C

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	14.1 g/L	ALOGPS
logP	-4.1	ALOGPS
logP	-5.5	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.85	ChemAxon
pKa (Strongest Basic)	9.83	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	126.64 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	43.64 m³·mol⁻¹	ChemAxon
Polarizability	18.93 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:

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
N-succinyl-L-2,6-diaminoheptanedioate + Water > Succinic acid + Diaminopimelic acid
Diaminopimelic acid > Meso-2,6-Diaminoheptanedioate
N-Succinyl-L,L-2,6-diaminopimelate + Water > Succinic acid + Diaminopimelic acid
Water + N-Succinyl-L,L-2,6-diaminopimelate <> Diaminopimelic acid + Succinic acid

SMPDB Pathways:

Lysine biosynthesis

PW000771

KEGG Pathways:

Lysine biosynthesis ec00300
Metabolic pathways eco01100
Microbial metabolism in diverse environments ec01120

EcoCyc Pathways:

lysine biosynthesis I DAPLYSINESYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0umi-1950000000-749403a0eb6d05c7903e	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0uk9-1980000000-1b092f9141e7549bee24	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0umi-1950000000-749403a0eb6d05c7903e	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uk9-1980000000-1b092f9141e7549bee24	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dm-9500000000-5d0aafd0747a1090e055	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-014i-4590000000-b941e92697a8b7800912	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004l-0900000000-d85213bd7ac426f10cd7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-9100000000-add590f1b216bdb40334	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-001i-9000000000-de98ed3bb8c48b6f9852	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-2c8a0ca138ef6ea5ef43	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-003r-9600000000-19f54d2417fe44d0eba3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-e8b0bbffeaa501a6fedd	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-91296097628a67dd97ef	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-e5c4e034dcab0695e0ce	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-002r-0900000000-2a19445fee9eade1d538	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9000000000-f44538bc8ae3a51cbbc6	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-003r-9700000000-3baa36a29b4ed6172da0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-1900000000-cf39d89ce72ac9ddaf51	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0200-6900000000-6f21b7798408480c1bfc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9300000000-6e778092666f89ff4211	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-28fbb202ae5558af7594	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-004i-1900000000-8a1ee3da7fbe94f840c2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-8caae42eda716644fdc1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0005-1900000000-be94a16bee7fad24d5d9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-5900000000-896859ce722942f9dd68	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006t-9200000000-50c1b5a4f7b19e8ff0db	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-5ecd829b51ba774883f6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-1900000000-53b7aee01233b5b73d3e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9400000000-2cc35eb21a44b2d472b5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0079-0900000000-a0ce1f9601e9b8d83ccf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dj-6900000000-cc22f522673c5549366c	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	View in JSpectraViewer

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)

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Links

External Links:

Resource	Link
CHEBI ID	23673
HMDB ID	HMDB01370
Pubchem Compound ID	865
Kegg ID	C00666
ChemSpider ID	388416
Wikipedia ID	Diaminopimelic acid
BioCyc ID	LL-DIAMINOPIMELATE
EcoCyc ID	LL-DIAMINOPIMELATE

Enzymes

Protein Details

1. Diaminopimelate decarboxylase

General function:: Involved in catalytic activity
Specific function:: Meso-2,6-diaminoheptanedioate = L-lysine + CO(2)
Gene Name:: lysA
Uniprot ID:: P00861
Molecular weight:: 46177

Reactions

Meso-2,6-diaminoheptanedioate = L-lysine + CO(2).

Protein Details

2. Diaminopimelate epimerase

General function:: Involved in diaminopimelate epimerase activity
Specific function:: LL-2,6-diaminoheptanedioate = meso- diaminoheptanedioate
Gene Name:: dapF
Uniprot ID:: P0A6K1
Molecular weight:: 30208

Reactions

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.

Protein Details

3. 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
Uniprot ID:: P0AED7
Molecular weight:: 41269

Reactions

N-succinyl-LL-2,6-diaminoheptanedioate + H(2)O = succinate + LL-2,6-diaminoheptanedioate.

Protein Details

4. 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
Uniprot ID:: P22188
Molecular weight:: 53343

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.

Protein Details

5. Protein mpaA

General function:: Involved in metallocarboxypeptidase activity
Specific function:: Specific function unknown
Gene Name:: mpaA
Uniprot ID:: P0ACV6
Molecular weight:: 26558

Transporters

Protein Details

1. Diaminopimelate epimerase

General function:: Involved in diaminopimelate epimerase activity
Specific function:: LL-2,6-diaminoheptanedioate = meso- diaminoheptanedioate
Gene Name:: dapF
Uniprot ID:: P0A6K1
Molecular weight:: 30208

Reactions

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.

Protein Details

2. Outer membrane protein N

General function:: Involved in transporter activity
Specific function:: Non-specific porin
Gene Name:: ompN
Uniprot ID:: P77747
Molecular weight:: 41220

Protein Details

3. Outer membrane pore protein E

General function:: Involved in transporter activity
Specific function:: Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:: phoE
Uniprot ID:: P02932
Molecular weight:: 38922

Protein Details

4. Outer membrane protein F

General function:: Involved in transporter activity
Specific function:: OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:: ompF
Uniprot ID:: P02931
Molecular weight:: 39333

Protein Details

5. Outer membrane protein C

General function:: Involved in transporter activity
Specific function:: Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:: ompC
Uniprot ID:: P06996
Molecular weight:: 40368

Diaminopimelic acid (ECMDB01370) (M2MDB000360)

Structure for #<Compound:0xa5459034>

Enzymes

Reactions

Reactions

Reactions

Reactions

Transporters

Reactions