2.0 2012-05-31 14:21:24 -0600 2015-06-03 17:19:04 -0600 ECMDB12266 M2MDB000835 N-Succinyl-2-amino-6-ketopimelate N-Succinyl-2-amino-6-ketopimelate is an intermediate in lysine biosynthesis. It is the fourth to last step in n the synthesis of lysine and is converted from tetrahydrodipicolinate via the enzyme tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117). It is then converted to N-succinyl-L,L-2,6-diaminopimelate via the enzyme Succinyldiaminopimelate transferase (EC 2.6.1.17). (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioate (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid (S)-2-(Succinylamino)-6-oxoheptanedioate (S)-2-(Succinylamino)-6-oxoheptanedioic acid <i>N</i>-succinyl-L-2-amino-6-oxoheptanedioate L-2-Succinylamino-6-oxoheptanedioate L-2-Succinylamino-6-oxoheptanedioic acid N-Succinyl-2-amino-6-ketopimelic acid N-Succinyl-2-amino-6-oxo-L-pimelate N-Succinyl-2-amino-6-oxo-L-pimelic acid N-Succinyl-2-L-amino-6-oxoheptanedioate N-Succinyl-2-L-amino-6-oxoheptanedioic acid N-Succinyl-epsilon-keto-L-aminopimelate N-Succinyl-epsilon-keto-L-aminopimelic acid N-Succinyl-L-2-amino-6-oxoheptanedioate N-Succinyl-L-2-amino-6-oxoheptanedioic acid N-Succinyl-L-2-amino-6-oxopimelate N-Succinyl-L-2-amino-6-oxopimelic acid SAKPA Succinyl-&epsilon;-keto-&alpha;-aminopimelate Succinyl-&epsilon;-keto-&alpha;-aminopimelic acid Succinyl-epsilon-keto-a-aminopimelate Succinyl-epsilon-keto-a-aminopimelic acid Succinyl-epsilon-keto-alpha-aminopimelate Succinyl-epsilon-keto-alpha-aminopimelic acid Succinyl-epsilon-keto-α-aminopimelate Succinyl-epsilon-keto-α-aminopimelic acid C11H15NO8 289.2387 289.079766461 (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid OC(=O)CCC(=O)N[C@@H](CCCC(=O)C(O)=O)C(O)=O InChI=1S/C11H15NO8/c13-7(11(19)20)3-1-2-6(10(17)18)12-8(14)4-5-9(15)16/h6H,1-5H2,(H,12,14)(H,15,16)(H,17,18)(H,19,20)/t6-/m0/s1 SDVXSCSNVVZWDD-LURJTMIESA-N Solid Cytosol logp -0.78 ALOGPS logs -2.31 ALOGPS solubility 1.41e+00 g/l ALOGPS logp -0.55 ChemAxon pka_strongest_acidic 2.78 ChemAxon pka_strongest_basic -1.5 ChemAxon iupac (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid ChemAxon average_mass 289.2387 ChemAxon mono_mass 289.079766461 ChemAxon smiles OC(=O)CCC(=O)N[C@@H](CCCC(=O)C(O)=O)C(O)=O ChemAxon formula C11H15NO8 ChemAxon inchi InChI=1S/C11H15NO8/c13-7(11(19)20)3-1-2-6(10(17)18)12-8(14)4-5-9(15)16/h6H,1-5H2,(H,12,14)(H,15,16)(H,17,18)(H,19,20)/t6-/m0/s1 ChemAxon inchikey SDVXSCSNVVZWDD-LURJTMIESA-N ChemAxon polar_surface_area 158.07 ChemAxon refractivity 61.57 ChemAxon polarizability 25.89 ChemAxon rotatable_bond_count 10 ChemAxon acceptor_count 8 ChemAxon donor_count 4 ChemAxon physiological_charge -3 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 22403 Specdb::CMs 39889 Specdb::CMs 160574 Specdb::NmrOneD 96818 Specdb::NmrOneD 96819 Specdb::NmrOneD 96820 Specdb::NmrOneD 96821 Specdb::NmrOneD 96822 Specdb::NmrOneD 96823 Specdb::NmrOneD 96824 Specdb::NmrOneD 96825 Specdb::NmrOneD 96826 Specdb::NmrOneD 96827 Specdb::NmrOneD 96828 Specdb::NmrOneD 96829 Specdb::NmrOneD 96830 Specdb::NmrOneD 96831 Specdb::NmrOneD 96832 Specdb::NmrOneD 96833 Specdb::NmrOneD 96834 Specdb::NmrOneD 96835 Specdb::NmrOneD 96836 Specdb::NmrOneD 96837 Specdb::MsMs 26825 Specdb::MsMs 26826 Specdb::MsMs 26827 Specdb::MsMs 33383 Specdb::MsMs 33384 Specdb::MsMs 33385 Specdb::MsMs 2421024 Specdb::MsMs 2421025 Specdb::MsMs 2421026 Specdb::MsMs 2544595 Specdb::MsMs 2544596 Specdb::MsMs 2544597 HMDB12266 440349 389314 C04462 N-SUCCINYL-2-AMINO-6-KETOPIMELATE 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 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase P0A9D8 DAPD_ECOLI dapD http://ecmdb.ca/proteins/P0A9D8.xml Acetylornithine/succinyldiaminopimelate aminotransferase P18335 ARGD_ECOLI argD http://ecmdb.ca/proteins/P18335.xml Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate R04365 TETHYDPICSUCC-RXN alpha-Ketoglutarate + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate R04475 Oxoglutaric acid + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate SUCCINYLDIAMINOPIMTRANS-RXN N-succinyl-L-2,6-diaminoheptanedioate + Oxoglutaric acid > N-Succinyl-2-amino-6-ketopimelate + L-Glutamate Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + Water > CoA + N-Succinyl-2-amino-6-ketopimelate (S)-2,3,4,5-tetrahydrodipicolinate + Succinyl-CoA + Water + Succinyl-CoA > Coenzyme A + N-Succinyl-2-amino-6-ketopimelate PW_R002529 N-Succinyl-2-amino-6-ketopimelate + L-Glutamic acid + L-Glutamate > N-Succinyl-L,L-2,6-diaminopimelate + Oxoglutaric acid PW_R002530 alpha-Ketoglutarate + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate