2.0 2012-05-31 13:51:08 -0600 2015-09-13 12:56:11 -0600 ECMDB01370 M2MDB000360 Diaminopimelic acid 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. ( (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 C7H14N2O4 190.1971 190.095356946 (2S,6S)-2,6-diaminoheptanedioic acid diamino-pimelic acid 583-93-7 N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O 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 GMKMEZVLHJARHF-WHFBIAKZSA-N Solid Cytosol Extra-organism Periplasm logp -4.13 ALOGPS logs -1.13 ALOGPS solubility 1.41e+01 g/l ALOGPS melting_point 300 oC logp -5.5 ChemAxon pka_strongest_acidic 1.85 ChemAxon pka_strongest_basic 9.83 ChemAxon iupac (2S,6S)-2,6-diaminoheptanedioic acid ChemAxon average_mass 190.1971 ChemAxon mono_mass 190.095356946 ChemAxon smiles N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O ChemAxon formula C7H14N2O4 ChemAxon 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 ChemAxon inchikey GMKMEZVLHJARHF-WHFBIAKZSA-N ChemAxon polar_surface_area 126.64 ChemAxon refractivity 43.64 ChemAxon polarizability 18.93 ChemAxon rotatable_bond_count 6 ChemAxon acceptor_count 6 ChemAxon donor_count 4 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Lysine biosynthesis Lysine is biosynthesized from L-aspartic acid. L-aspartic acid can be incorporated into the cell through various methods: C4 dicarboxylate / orotate:H+ symporter , glutamate / aspartate : H+ symporter GltP, dicarboxylate transporter , C4 dicarboxylate / C4 monocarboxylate transporter DauA, glutamate / aspartate ABC transporter L-aspartic acid is phosphorylated by an ATP-driven Aspartate kinase resulting in ADP and L-aspartyl-4-phosphate. L-aspartyl-4-phosphate is then dehydrogenated through an NADPH driven aspartate semialdehyde dehydrogenase resulting in a release of phosphate, NADP and L-aspartic 4-semialdehyde (involved in methionine biosynthesis). L-aspartic 4-semialdehyde interacts with a pyruvic acid through a 4-hydroxy-tetrahydrodipicolinate synthase resulting in a release of hydrogen ion, water and (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate. The latter compound is then reduced by an NADPH driven 4-hydroxy-tetrahydrodipicolinate reductase resulting in a release of water, NADP and (S)-2,3,4,5-tetrahydrodipicolinate, This compound interacts with succinyl-CoA and water through a tetrahydrodipicolinate succinylase resulting in a release of coenzyme A and N-Succinyl-2-amino-6-ketopimelate. This compound interacts with L-glutamic acid through a N-succinyldiaminopimelate aminotransferase resulting in oxoglutaric acid, N-succinyl-L,L-2,6-diaminopimelate. The latter compound is then desuccinylated by reacting with water through a N-succinyl-L-diaminopimelate desuccinylase resulting in a succinic acid and L,L-diaminopimelate. This compound is then isomerized through a diaminopimelate epimerase resulting in a meso-diaminopimelate (involved in peptidoglyccan biosynthesis I). This compound is then decarboxylated by a diaminopimelate decarboxylase resulting in a release of carbon dioxide and L-lysine. L-lysine is then incorporated into lysine degradation pathway. Lysine also regulate its own biosynthesis by repressing dihydrodipicolinate synthase and also repressing lysine-sensitive aspartokinase 3. A metabolic connection joins synthesis of an amino acid, lysine, to synthesis of cell wall material. Diaminopimelate is a precursor both for lysine and for cell wall components. The synthesis of lysine, methionine and threonine share two reactions at the start of the three pathways, the reactions converting L-aspartate to L-aspartate semialdehyde. The reaction involving aspartate kinase is carried out by three isozymes, one specific for synthesis of each end product amino acid. Each of the three aspartate kinase isozymes is regulated by its corresponding end product amino acid. PW000771 ec00300 Metabolic Microbial metabolism in diverse environments ec01120 Metabolic pathways eco01100 lysine biosynthesis I DAPLYSINESYN-PWY Specdb::CMs 731 Specdb::CMs 732 Specdb::CMs 2666 Specdb::CMs 30185 Specdb::CMs 30251 Specdb::CMs 38043 Specdb::CMs 170469 Specdb::NmrOneD 1690 Specdb::NmrOneD 147590 Specdb::NmrOneD 147591 Specdb::NmrOneD 147592 Specdb::NmrOneD 147593 Specdb::NmrOneD 147594 Specdb::NmrOneD 147595 Specdb::NmrOneD 147596 Specdb::NmrOneD 147597 Specdb::NmrOneD 147598 Specdb::NmrOneD 147599 Specdb::NmrOneD 147600 Specdb::NmrOneD 147601 Specdb::NmrOneD 147602 Specdb::NmrOneD 147603 Specdb::NmrOneD 147604 Specdb::NmrOneD 147605 Specdb::NmrOneD 147606 Specdb::NmrOneD 147607 Specdb::NmrOneD 147608 Specdb::NmrOneD 147609 Specdb::MsMs 1538 Specdb::MsMs 1539 Specdb::MsMs 1540 Specdb::MsMs 182697 Specdb::MsMs 182698 Specdb::MsMs 182699 Specdb::MsMs 183045 Specdb::MsMs 183046 Specdb::MsMs 183047 Specdb::MsMs 2240765 Specdb::MsMs 2240913 Specdb::MsMs 2244429 Specdb::MsMs 2244985 Specdb::MsMs 2245142 Specdb::MsMs 2245662 Specdb::MsMs 2246531 Specdb::MsMs 2247026 Specdb::MsMs 2247250 Specdb::MsMs 2247766 Specdb::MsMs 2249147 Specdb::MsMs 2249249 Specdb::MsMs 2251176 Specdb::MsMs 2251216 Specdb::MsMs 2330745 Specdb::MsMs 2330746 Specdb::NmrTwoD 1631 HMDB01370 865 388416 C00666 23673 LL-DIAMINOPIMELATE 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. 21097882 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. 22080510 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. 17765195 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. 16166681 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. 6118181 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. 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. 1656007 Gao, Yong. Synthesis of diaminopimelic acid (DAP) and analogues: mechanistic studies on DAP aminotransferase, epimerase and dehydrogenase. (1998), 166 pp. http://hmdb.ca/system/metabolites/msds/000/001/232/original/HMDB01370.pdf?1358461364 Diaminopimelate decarboxylase P00861 DCDA_ECOLI lysA http://ecmdb.ca/proteins/P00861.xml Diaminopimelate epimerase P0A6K1 DAPF_ECOLI dapF http://ecmdb.ca/proteins/P0A6K1.xml Succinyl-diaminopimelate desuccinylase P0AED7 DAPE_ECOLI dapE http://ecmdb.ca/proteins/P0AED7.xml UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase P22188 MURE_ECOLI murE http://ecmdb.ca/proteins/P22188.xml Protein mpaA P0ACV6 MPAA_ECOLI mpaA http://ecmdb.ca/proteins/P0ACV6.xml Diaminopimelate epimerase P0A6K1 DAPF_ECOLI dapF http://ecmdb.ca/proteins/P0A6K1.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Outer membrane pore protein E P02932 PHOE_ECOLI phoE http://ecmdb.ca/proteins/P02932.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml 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 R02734 SUCCDIAMINOPIMDESUCC-RXN Diaminopimelic acid + Hydrogen ion > Carbon dioxide + L-Lysine Diaminopimelic acid <> Meso-2,6-Diaminoheptanedioate R02735 Diaminopimelic acid <> <i>meso</i>-diaminopimelate DIAMINOPIMEPIM-RXN 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 PW_R002531 Water + N-Succinyl-L,L-2,6-diaminopimelate <> Diaminopimelic acid + Succinic acid