2.0 2012-05-31 14:21:40 -0600 2015-06-03 17:19:04 -0600 ECMDB12289 M2MDB000840 Tetrahydrodipicolinate Tetrahydrodipicolinate is involved in amino-acid biosynthesis, specifically L-lysine biosynthesis via the DAP pathway Δ1-piperideine-2,6-dicarboxylate Δ1-piperideine-2,6-dicarboxylic acid Δ1-piperideine-2,6-dicarboxylate (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid 2,3,4,5-Tetrahydro-2,6-dipicolinate 2,3,4,5-Tetrahydro-2,6-dipicolinic acid 2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylate 2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acid 2,3,4,5-Tetrahydrodipicolinate 2,3,4,5-Tetrahydrodipicolinic acid 2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate 2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acid 2,3,4,5-THDPA Delta1-piperideine-2,6-dicarboxylate Delta1-piperideine-2,6-dicarboxylic acid L-2,3,4,5-Tetrahydrodipicolinate L-2,3,4,5-Tetrahydrodipicolinic acid Tetrahydrodipicolinate Tetrahydrodipicolinic acid Tetrahydropyridine-2,6-dicarboxylate Tetrahydropyridine-2,6-dicarboxylic acid Thdpa δ1-Piperideine-2,6-dicarboxylate δ1-Piperideine-2,6-dicarboxylic acid C7H9NO4 171.1507 171.053157781 2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid thdpa 2353-17-5 OC(=O)C1CCCC(=N1)C(O)=O InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12) CXMBCXQHOXUCEO-UHFFFAOYSA-N Solid Cytosol logp 0.18 ALOGPS logs -1.42 ALOGPS solubility 6.49e+00 g/l ALOGPS logp 0.66 ChemAxon pka_strongest_acidic 3.28 ChemAxon pka_strongest_basic -2 ChemAxon iupac 2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid ChemAxon average_mass 171.1507 ChemAxon mono_mass 171.053157781 ChemAxon smiles OC(=O)C1CCCC(=N1)C(O)=O ChemAxon formula C7H9NO4 ChemAxon inchi InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12) ChemAxon inchikey CXMBCXQHOXUCEO-UHFFFAOYSA-N ChemAxon polar_surface_area 86.96 ChemAxon refractivity 38.27 ChemAxon polarizability 15.74 ChemAxon rotatable_bond_count 2 ChemAxon acceptor_count 5 ChemAxon donor_count 2 ChemAxon physiological_charge -2 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 Monobactam biosynthesis eco00261 Metabolic pathways eco01100 lysine biosynthesis I DAPLYSINESYN-PWY Specdb::CMs 11159 Specdb::CMs 39902 Specdb::NmrOneD 324592 Specdb::NmrOneD 324593 Specdb::NmrOneD 324594 Specdb::NmrOneD 324595 Specdb::NmrOneD 324596 Specdb::NmrOneD 324597 Specdb::NmrOneD 324598 Specdb::NmrOneD 324599 Specdb::NmrOneD 324600 Specdb::NmrOneD 324601 Specdb::NmrOneD 324602 Specdb::NmrOneD 324603 Specdb::NmrOneD 324604 Specdb::NmrOneD 324605 Specdb::NmrOneD 324606 Specdb::NmrOneD 324607 Specdb::NmrOneD 324608 Specdb::NmrOneD 324609 Specdb::NmrOneD 324610 Specdb::NmrOneD 324611 Specdb::MsMs 28871 Specdb::MsMs 28872 Specdb::MsMs 28873 Specdb::MsMs 35429 Specdb::MsMs 35430 Specdb::MsMs 35431 HMDB12289 632 612 C03972 32976 DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE 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 Dihydrodipicolinate reductase P04036 DAPB_ECOLI dapB http://ecmdb.ca/proteins/P04036.xml 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase P0A9D8 DAPD_ECOLI dapD http://ecmdb.ca/proteins/P0A9D8.xml 2,3-Dihydrodipicolinic acid + Hydrogen ion + NADPH > NADP + Tetrahydrodipicolinate R04199 Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate R04365 TETHYDPICSUCC-RXN Tetrahydrodipicolinate + NAD <> 2,3-Dihydrodipicolinic acid + NADH + Hydrogen ion R04198 Tetrahydrodipicolinate + NADP <> 2,3-Dihydrodipicolinic acid + NADPH + Hydrogen ion R04199 NAD(P)+ + Tetrahydrodipicolinate < NAD(P)H + 2,3-Dihydrodipicolinic acid + Hydrogen ion DIHYDROPICRED-RXN Hydrogen ion + Tetrahydrodipicolinate + Water > L-α-amino-ε-keto-pimelate RXN-4821 Tetrahydrodipicolinate + NAD + NADP + Water <> (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + NADPH + Hydrogen ion R04198 R04199 Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate 2 2,3-Dihydrodipicolinic acid + Hydrogen ion + NADPH > NADP + Tetrahydrodipicolinate