2.0 2012-05-31 10:23:06 -0600 2015-09-13 12:56:06 -0600 ECMDB00182 M2MDB000075 L-Lysine L-lysine is an alpha-amino acid with the chemical formula HO2CCH(NH2)(CH2)4NH2. Lysine is a basic amino acid as are arginine and histidine. Lysine is a proteogenic amino acid, meaning that it is used in protein synthesis. Lysine typically constitutes about 7-8% of an average protein. The epsilon-amino group often participates in hydrogen bonding and as a general base in catalysis. Common posttranslational modifications include methylation of the epsilon-amino group, giving methyl-, dimethyl-, and trimethyllysine. In bacteria, lysine is synthesized from aspartic acid, which is first converted to aspartyl-semialdehyde. (+)-S-Lysine (S)-2,6-diamino-Hexanoate (S)-2,6-diamino-Hexanoic acid (S)-2,6-Diaminohexanoate (S)-2,6-Diaminohexanoic acid (S)-a,e-Diaminocaproate (S)-a,e-Diaminocaproic acid (S)-Lysine 2,6-Diaminohexanoate 2,6-Diaminohexanoic acid 6-Amino-Aminutrin 6-Amino-L-Norleucine A-Lysine Alpha-Lysine Aminutrin H-Lys-oh K L-(+)-Lysine L-2,6-Diainohexanoate L-2,6-Diainohexanoic acid L-2,6-Diaminocaproate L-2,6-Diaminocaproic acid L-Lys Lys Lysine Lysine acid α-Lysine C6H14N2O2 146.1876 146.105527702 (2S)-2,6-diaminohexanoic acid L-lysine 56-87-1 NCCCC[C@H](N)C(O)=O InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1 KDXKERNSBIXSRK-YFKPBYRVSA-N Solid Cytosol Extra-organism Periplasm logp -3.76 ALOGPS logs -0.14 ALOGPS solubility 1.05e+02 g/l ALOGPS melting_point 224.5 oC logp -3.2 ChemAxon pka_strongest_acidic 2.74 ChemAxon pka_strongest_basic 10.29 ChemAxon iupac (2S)-2,6-diaminohexanoic acid ChemAxon average_mass 146.1876 ChemAxon mono_mass 146.105527702 ChemAxon smiles NCCCC[C@H](N)C(O)=O ChemAxon formula C6H14N2O2 ChemAxon inchi InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1 ChemAxon inchikey KDXKERNSBIXSRK-YFKPBYRVSA-N ChemAxon polar_surface_area 89.34 ChemAxon refractivity 37.81 ChemAxon polarizability 15.84 ChemAxon rotatable_bond_count 5 ChemAxon acceptor_count 4 ChemAxon donor_count 3 ChemAxon physiological_charge 1 ChemAxon formal_charge 0 ChemAxon Tropane, piperidine and pyridine alkaloid biosynthesis ec00960 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 Aminoacyl-tRNA biosynthesis ec00970 Biotin metabolism Biotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases, such as pyruvate carboxylase and acetyl-CoA carboxylase.In E. coli and many organisms, pimelate thioester is derived from malonyl-ACP. The pathway starts with a malonyl-[acp] interacting with S-adenosylmethionine through a biotin synthesis protein BioC resulting in a S-adenosylhomocysteine and a malonyl-[acp] methyl ester. The latter compound is then involved in the synthesis of a 3-ketoglutaryl-[acp] methyl ester through a 3-oxoacyl-[acyl-carrier-protein] synthase. The compound 3-ketoglutaryl-[acp] methyl ester is reduced by a NADPH mediated 3-oxoacyl-[acyl-carrier-protein] reductase resulting in a 3R-hydroxyglutaryl-[acp] methyl ester. This compound is then dehydrated through ad (3R)-hydroxymyristoyl-[acp] dehydratase producing a enoylglutaryl-[acp] methyl ester. This compound is then reduced through a NADPH mediated enoyl-acp-reductase [NADH] resulting in a glutaryl-[acp] methyl ester. This compound interacts with a malonyl-[acp] through a 3-oxoacyl-[acp] synthase 2 resulting in a 3-ketopimeloyl [acp] methyl ester. This compound is then reduced through a NADPH 3-oxoacyl [acp] reductase producing a 3-hydroxypimeloyl-[acp] methyl ester and then dehydrated by (3R)-hydroxymyristoyl-[acp] dehydratase to produce a enoylpimeloyl-[acp] methyl ester. This compound is then reduced by a NADPH dependent enoyl-[acp]reductase resulting in a pimeloyl-[acp] methyl ester. This compound then reacts with water through a carboxylesterase resulting in a pimeloyl-[acp] and a methanol. The pimeloyl-acp reacts with L-alanine through a 8-amino-7-oxononanoate synthase resulting in 8-amino-7-oxononanoate which in turn reacts with S-adenosylmethionine through a 7,8 diaminonanoate transaminase resulting in a S-adenosyl-4-methylthio-2-oxobutanoate and 7,8 diaminononanoate. The latter compound is then dephosphorylated through a dethiobiotin synthetase resulting in a dethiobiotin. This compound interacts with a sulfurated[sulfur carrier), a hydrogen ion and a S-adenosylmethionine through a biotin synthase to produce Biotin and releasing l-methionine and a 5-deoxyadenosine. Biotin is then metabolized by a bifunctional protein resulting in pyrophosphate and Biotinyl-5-AMP which in turn reacts with the same protein (bifunctional protein birA resulting ina biotin caroxyl carrying protein.This product then enters the fatty acid biosynthesis. PW000762 ec00780 Metabolic Lysine degradation ec00310 Microbial metabolism in diverse environments ec01120 ABC transporters ec02010 Metabolic pathways eco01100 Lysine Degradation I Under conditions of anaerobiosis and phosphate starvation (believed to reflect conditions in the gut), E. coli converts glucose to weak organic acids which, though they are excreted, can reenter the cell and cause bactericidal acid stress even at only moderately acidic pH. Acid resistance system 4 (AR4) is the lysine-dependent acid resistance system which allows for the survival of E. coli under these conditions when lysine is available. AR4 couples the transport activity of a lysine:cadaverine antiporter, CadB, with lysine decarboxylase, CadA. CadB functions by exchanging external lysine for internal cadaverine. Lysine is imported into the cell through CadB or generated in the cell from aspartic acid. Within the cell, lysine is decarboxylated by CadA to cadaverine, releasing CO2 and replacing it with a proton. Cadaverine is then exported through CadB. This effectively consumes protons within the cytoplasm, raising the pH. The glutamate-dependent acid resistance system (AR2) is also able to provide acid resistance to E. coli growing under conditions of anaerobiosis and phosphate starvation, but to a slightly lesser degree than AR4 possibly due to the different pH optimums of their respective decarboxylase enzymes. AR2 is more efficient than AR3 or AR4 as a mediator of acid resistance at low pH. PW000772 Metabolic inner membrane transport list of inner membrane transport complexes, transporting compounds from the periplasmic space to the cytosol This pathway should be updated regularly with the new inner membrae transports added PW000786 Metabolic tRNA Charging 2 This pathway groups together all E. coli tRNA charging reactions. PW000803 Metabolic tRNA charging This pathway groups together all E. coli tRNA charging reactions. PW000799 Metabolic Fructoselysine and Psicoselysine Degradation Fructosamines are generated non-enzymatically by a condensation of glucose with primary amines, followed by an Amadori rearrangement. Fructoselysine appears to be metabolized by bacteria in the human hind gut. E. coli can grow on fructoselysine or psicoselysine as the sole carbon source. Growth on fructoselysine induces the production of the enzymes of the fructoselysine degradation pathway. (EcoCyc) PW002049 Metabolic aminopropylcadaverine biosynthesis Polyamines are important for cell growth and are believed to be involved in many processes including DNA, RNA, and protein synthesis, as well as membrane integrity and resistance to stress, to name a few. Cadaverine and aminopropylcadaverine are alternative polyamines that can at least partially substitute for purtrescine and spermidine, the primary polyamines found in E. coli. Lysine is decarboxylated to form cadaverine which is then converted to aminopropylcadaverine by the aminopropyltransferase, SpeE. (EcoCyc) PW002039 Metabolic tRNA charging TRNA-CHARGING-PWY lysine biosynthesis I DAPLYSINESYN-PWY fructoselysine and psicoselysine degradation PWY0-521 aminopropylcadaverine biosynthesis PWY0-1303 lysine degradation I PWY0-461 Specdb::CMs 423 Specdb::CMs 424 Specdb::CMs 425 Specdb::CMs 1365 Specdb::CMs 1547 Specdb::CMs 1644 Specdb::CMs 2495 Specdb::CMs 30111 Specdb::CMs 30112 Specdb::CMs 30377 Specdb::CMs 30602 Specdb::CMs 30737 Specdb::CMs 30794 Specdb::CMs 31054 Specdb::CMs 31055 Specdb::CMs 31056 Specdb::CMs 32353 Specdb::CMs 37342 Specdb::CMs 148423 Specdb::CMs 1052863 Specdb::CMs 1052865 Specdb::CMs 1052867 Specdb::CMs 1052869 Specdb::CMs 1052871 Specdb::NmrOneD 1151 Specdb::NmrOneD 1194 Specdb::NmrOneD 4846 Specdb::NmrOneD 142750 Specdb::NmrOneD 142751 Specdb::NmrOneD 142752 Specdb::NmrOneD 142753 Specdb::NmrOneD 142754 Specdb::NmrOneD 142755 Specdb::NmrOneD 142756 Specdb::NmrOneD 142757 Specdb::NmrOneD 142758 Specdb::NmrOneD 142759 Specdb::NmrOneD 142760 Specdb::NmrOneD 142761 Specdb::NmrOneD 142762 Specdb::NmrOneD 142763 Specdb::NmrOneD 142764 Specdb::NmrOneD 142765 Specdb::NmrOneD 142766 Specdb::NmrOneD 142767 Specdb::NmrOneD 142768 Specdb::NmrOneD 142769 Specdb::NmrOneD 166351 Specdb::NmrOneD 166447 Specdb::MsMs 289 Specdb::MsMs 290 Specdb::MsMs 291 Specdb::MsMs 3408 Specdb::MsMs 3409 Specdb::MsMs 3410 Specdb::MsMs 3411 Specdb::MsMs 3412 Specdb::MsMs 3413 Specdb::MsMs 3414 Specdb::MsMs 3415 Specdb::MsMs 3416 Specdb::MsMs 3417 Specdb::MsMs 3418 Specdb::MsMs 3419 Specdb::MsMs 3420 Specdb::MsMs 3421 Specdb::MsMs 3422 Specdb::MsMs 3423 Specdb::MsMs 3424 Specdb::MsMs 3425 Specdb::MsMs 3429 Specdb::MsMs 3430 Specdb::MsMs 3431 Specdb::MsMs 3432 Specdb::NmrTwoD 985 Specdb::NmrTwoD 1191 HMDB00182 5962 5747 C00047 18019 LYS LYS_LFZW_DHZ3 L-Lysine 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 Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. 18402659 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 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. 17379776 Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. 19212411 Silwood CJ, Lynch E, Claxson AW, Grootveld MC: 1H and (13)C NMR spectroscopic analysis of human saliva. J Dent Res. 2002 Jun;81(6):422-7. 12097436 Nicholson JK, O'Flynn MP, Sadler PJ, Macleod AF, Juul SM, Sonksen PH: Proton-nuclear-magnetic-resonance studies of serum, plasma and urine from fasting normal and diabetic subjects. Biochem J. 1984 Jan 15;217(2):365-75. 6696735 Engelborghs S, Marescau B, De Deyn PP: Amino acids and biogenic amines in cerebrospinal fluid of patients with Parkinson's disease. Neurochem Res. 2003 Aug;28(8):1145-50. 12834252 Hagenfeldt L, Bjerkenstedt L, Edman G, Sedvall G, Wiesel FA: Amino acids in plasma and CSF and monoamine metabolites in CSF: interrelationship in healthy subjects. J Neurochem. 1984 Mar;42(3):833-7. 6198473 Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. 15911239 Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. 12297216 Rainesalo S, Keranen T, Palmio J, Peltola J, Oja SS, Saransaari P: Plasma and cerebrospinal fluid amino acids in epileptic patients. Neurochem Res. 2004 Jan;29(1):319-24. 14992292 Kranz BR: Detection of rare malignant cells and their apoptotic fragments in cerebrospinal fluid. Lancet. 2000 Oct 7;356(9237):1242-4. 11072949 Hajishengallis G, Koga T, Russell MW: Affinity and specificity of the interactions between Streptococcus mutans antigen I/II and salivary components. J Dent Res. 1994 Sep;73(9):1493-502. 7523469 Pahler A, Parker J, Dekant W: Dose-dependent protein adduct formation in kidney, liver, and blood of rats and in human blood after perchloroethene inhalation. Toxicol Sci. 1999 Mar;48(1):5-13. 10330678 Faraasen S, Voros J, Csucs G, Textor M, Merkle HP, Walter E: Ligand-specific targeting of microspheres to phagocytes by surface modification with poly(L-lysine)-grafted poly(ethylene glycol) conjugate. Pharm Res. 2003 Feb;20(2):237-46. 12636162 Rothstein, Morton. DL-Lysine-6-C14 and DL-a-aminoadipic acid-6-C14. Biochemical Preparations (1961), 8 85-8. http://hmdb.ca/system/metabolites/msds/000/000/128/original/HMDB00182.pdf?1358461504 Diaminopimelate decarboxylase P00861 DCDA_ECOLI lysA http://ecmdb.ca/proteins/P00861.xml Histidine transport ATP-binding protein hisP P07109 HISP_ECOLI hisP http://ecmdb.ca/proteins/P07109.xml Lysyl-tRNA synthetase P0A8N3 SYK1_ECOLI lysS http://ecmdb.ca/proteins/P0A8N3.xml Lysyl-tRNA synthetase, heat inducible P0A8N5 SYK2_ECOLI lysU http://ecmdb.ca/proteins/P0A8N5.xml Uncharacterized protein YjeA P0A8N7 YJEA_ECOLI poxA http://ecmdb.ca/proteins/P0A8N7.xml Lysine decarboxylase, inducible P0A9H3 LDCI_ECOLI cadA http://ecmdb.ca/proteins/P0A9H3.xml Fructoselysine 6-phosphate deglycase P0AC00 FRLB_ECOLI frlB http://ecmdb.ca/proteins/P0AC00.xml Lysine decarboxylase, constitutive P52095 DCLZ_ECOLI ldcC http://ecmdb.ca/proteins/P52095.xml Histidine transport system permease protein hisM P0AEU3 HISM_ECOLI hisM http://ecmdb.ca/proteins/P0AEU3.xml Histidine transport system permease protein hisQ P52094 HISQ_ECOLI hisQ http://ecmdb.ca/proteins/P52094.xml Lysine-arginine-ornithine-binding periplasmic protein P09551 ARGT_ECOLI argT http://ecmdb.ca/proteins/P09551.xml tRNA(Ile)-lysidine synthetase (EC:6.1.1.5) P52097 tilS http://ecmdb.ca/proteins/P52097.xml Histidine transport ATP-binding protein hisP P07109 HISP_ECOLI hisP http://ecmdb.ca/proteins/P07109.xml Uncharacterized amino-acid ABC transporter ATP-binding protein yecC P37774 YECC_ECOLI yecC http://ecmdb.ca/proteins/P37774.xml Inner membrane amino-acid ABC transporter permease protein yecS P0AFT2 YECS_ECOLI yecS http://ecmdb.ca/proteins/P0AFT2.xml Histidine transport system permease protein hisM P0AEU3 HISM_ECOLI hisM http://ecmdb.ca/proteins/P0AEU3.xml Lysine-specific permease P25737 LYSP_ECOLI lysP http://ecmdb.ca/proteins/P25737.xml Histidine transport system permease protein hisQ P52094 HISQ_ECOLI hisQ http://ecmdb.ca/proteins/P52094.xml Lysine-arginine-ornithine-binding periplasmic protein P09551 ARGT_ECOLI argT http://ecmdb.ca/proteins/P09551.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 Probable cadaverine/lysine antiporter P0AAE8 CADB_ECOLI cadB http://ecmdb.ca/proteins/P0AAE8.xml Arginine exporter protein ArgO P11667 ARGO_ECOLI argO http://ecmdb.ca/proteins/P11667.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml Hydrogen ion + L-Lysine <> Cadaverine + Carbon dioxide R00462 LYSDECARBOX-RXN Adenosine triphosphate + Water + L-Lysine > ADP + Hydrogen ion + L-Lysine + Phosphate ABC-3-RXN Adenosine triphosphate + Water + L-Lysine > ADP + Hydrogen ion + L-Lysine + Phosphate ABC-3-RXN Adenosine triphosphate + L-Lysine + tRNA(Lys) > Adenosine monophosphate + L-Lysine-tRNA (Lys) + Pyrophosphate Diaminopimelic acid + Hydrogen ion > Carbon dioxide + L-Lysine Fructoselysine-6-phosphate + Water <> Glucose 6-phosphate + L-Lysine RXN0-963 Meso-2,6-Diaminoheptanedioate <> L-Lysine + Carbon dioxide R00451 L-Lysine <> Cadaverine + Carbon dioxide R00462 Adenosine triphosphate + L-Lysine + tRNA(Lys) + tRNA(Lys) <> Adenosine monophosphate + Pyrophosphate + L-Lysyl-tRNA + L-Lysyl-tRNA R03658 [tRNA(Ile2)]-cytidine34 + L-Lysine + Adenosine triphosphate <> [tRNA(Ile2)]-lysidine34 + Adenosine monophosphate + Pyrophosphate + Water R09597 L-Lysine + Adenosine triphosphate + Water > L-Lysine + ADP + Phosphate + Hydrogen ion ABC-3-RXN L-Lysine + Adenosine triphosphate + Water > L-Lysine + ADP + Phosphate + Hydrogen ion ABC-3-RXN Hydrogen ion + <i>meso</i>-diaminopimelate > L-Lysine + Carbon dioxide DIAMINOPIMDECARB-RXN Hydrogen ion + L-Lysine > Carbon dioxide + Cadaverine LYSDECARBOX-RXN L-Lysine (R)-beta-lysine RXN0-5192 Meso-2,6-Diaminoheptanedioate > L-Lysine + Carbon dioxide L-Lysine > Cadaverine + Carbon dioxide L-Lysine > (R)-beta-lysine Fructoselysine-6-phosphate + Water > Glucose 6-phosphate + L-Lysine Adenosine triphosphate + L-Lysine + tRNA(Lys) > Adenosine monophosphate + Pyrophosphate + L-lysyl-tRNA(Lys) (tRNA(Ile2))-cytidine(34) + L-Lysine + Adenosine triphosphate > (tRNA(Ile2))-lysidine(34) + Adenosine monophosphate + Pyrophosphate + Water Biocytin + Water > Biotin + L-Lysine + L-Lysine PW_R002492 Meso-2,6-Diaminoheptanedioate + Hydrogen ion > L-Lysine + Carbon dioxide + L-Lysine PW_R002533 L-Lysine + Hydrogen ion + L-Lysine > Cadaverine + Carbon dioxide PW_R002534 L-Lysine + L-Lysine > Cadaverine PW_R002535 L-Lysine + Adenosine triphosphate + Hydrogen ion + tRNA(Lys) + L-Lysine > Adenosine monophosphate + Pyrophosphate + L-Lysyl-tRNA PW_R002840 L-Lysine + Adenosine triphosphate + Water + L-Lysine > Adenosine diphosphate + Phosphate + Hydrogen ion + L-Lysine + ADP PW_RCT000110 Fructoselysine-6-phosphate + Water <> β-D-glucose 6-phosphate + L-Lysine PW_R005985 Adenosine triphosphate + L-Lysine + tRNA(Lys) <> Adenosine monophosphate + Pyrophosphate + L-Lysyl-tRNA Meso-2,6-Diaminoheptanedioate <> L-Lysine + Carbon dioxide Adenosine triphosphate + L-Lysine + tRNA(Lys) <> Adenosine monophosphate + Pyrophosphate + L-Lysyl-tRNA Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose Shake flask and filter culture 401.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 1604000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerol Shake flask and filter culture 762.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 3048000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetate Shake flask and filter culture 554.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 2216000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L Gluco Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h 361.0 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 1444000 0 Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. 17379776 Luria-Bertani (LB) media Shake flask 567.33 uM true 31.5 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 2269333 126005 Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., Lowther, W. T. (2007). "Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function." Proc Natl Acad Sci U S A 104:9597-9602. 17535911