2.0 2012-05-31 13:02:13 -0600 2015-09-13 12:56:09 -0600 ECMDB00929 M2MDB000203 L-Tryptophan Tryptophan is an amino acid which is the precursor of serotonin. Plants and microorganisms commonly synthesize tryptophan from shikimic acid or anthranilate. The latter condenses with phosphoribosylpyrophosphate (PRPP), generating pyrophosphate as a by-product. After ring opening of the ribose moiety and following reductive decarboxylation, indole-3-glycerinephosphate is produced, which in turn is transformed into indole. In the last step, tryptophan synthase catalyzes the formation of tryptophan from indole and the amino acid, serine. Metabolism of tryptophan to serotonin requires nutrients such as vitamin B6, niacin and glutathione. Niacin is an important metabolite of tryptophan. (Wikipedia) (-)-tryptophan (2S)-2-amino-3-(1H-indol-3-yl)propanoate (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid (L)-tryptophan (S)-1H-Indole-3-alanine (S)-2-Amino-3-(3-indolyl)propionate (S)-2-Amino-3-(3-indolyl)propionic acid (S)-a-Amino-1H-indole-3-propanoate (S)-a-Amino-1H-indole-3-propanoic acid (S)-a-amino-b-(3-Indolyl)-propionate (S)-a-amino-b-(3-Indolyl)-propionic acid (S)-a-amino-b-indolepropionate (S)-a-amino-b-indolepropionic acid (S)-a-Aminoindole-3-propionate (S)-a-Aminoindole-3-propionic acid (S)-alpha-Amino-1H-indole-3-propanoate (S)-alpha-Amino-1H-indole-3-propanoic acid (S)-alpha-Amino-beta-(3-indolyl)-propionate (S)-alpha-Amino-beta-(3-indolyl)-propionic acid (S)-alpha-amino-beta-indolepropionate (S)-alpha-amino-beta-indolepropionic acid (S)-alpha-Aminoindole-3-propionate (S)-alpha-Aminoindole-3-propionic acid (S)-tryptophan (S)-α-amino-1H-Indole-3-propanoate (S)-α-amino-1H-Indole-3-propanoic acid (S)-α-amino-β-(3-Indolyl)-propionate (S)-α-amino-β-(3-Indolyl)-propionic acid (S)-α-amino-β-Indolepropionate (S)-α-amino-β-Indolepropionic acid (S)-α-Aminoindole-3-propionate (S)-α-Aminoindole-3-propionic acid 1-b-3-Indolylalanine 1-beta-3-Indolylalanine 1-β-3-Indolylalanine 1b-3-Indolylalanine 1beta-3-Indolylalanine 1H-Indole-3-Alanine 1β-3-Indolylalanine 2-Amino-3-indolylpropanate 2-Amino-3-indolylpropanic acid 2-Amino-3-indolylpropanoate 2-Amino-3-indolylpropanoic acid 3-(1H-Indol-3-yl)-L-Alanine 3-Indol-3-ylalanine a-Aminoindole-3-propionate a-Aminoindole-3-propionic acid Alpha'-Amino-3-indolepropionate Alpha'-Amino-3-indolepropionic acid Alpha-Aminoindole-3-propionate Alpha-Aminoindole-3-propionic acid Ardeytropin H-TRP-oh Indole-3-alanine Kalma L-(-)-Tryptophan L-a-amino-3-Indolepropionate L-a-amino-3-Indolepropionic acid L-a-Aminoindole-3-propionate L-a-Aminoindole-3-propionic acid L-alpha-Amino-3-indolepropionate L-alpha-Amino-3-indolepropionic acid L-alpha-Aminoindole-3-propionate L-alpha-Aminoindole-3-propionic acid L-b-3-Indolylalanine L-beta-3-Indolylalanine L-Tryptofan L-Tryptophan L-Tryptophane L-α-amino-3-Indolepropionate L-α-amino-3-Indolepropionic acid L-α-Aminoindole-3-propionate L-α-Aminoindole-3-propionic acid L-β-3-Indolylalanine Lopac-T-0254 Lyphan Optimax Pacitron Sedanoct Triptofano Trofan Trp Tryptacin Tryptan Tryptophan Tryptophane Tryptophanum W α-Aminoindole-3-propionate α-Aminoindole-3-propionic acid C11H12N2O2 204.2252 204.089877638 (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid L-tryptophan 73-22-3 N[C@@H](CC1=CNC2=CC=CC=C12)C(O)=O InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1 QIVBCDIJIAJPQS-VIFPVBQESA-N Solid Cytosol Extra-organism Periplasm logp -1.10 ALOGPS logs -2.18 ALOGPS solubility 1.36e+00 g/l ALOGPS melting_point 230 oC logp -1.1 ChemAxon pka_strongest_acidic 2.54 ChemAxon pka_strongest_basic 9.4 ChemAxon iupac (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid ChemAxon average_mass 204.2252 ChemAxon mono_mass 204.089877638 ChemAxon smiles N[C@@H](CC1=CNC2=CC=CC=C12)C(O)=O ChemAxon formula C11H12N2O2 ChemAxon inchi InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1 ChemAxon inchikey QIVBCDIJIAJPQS-VIFPVBQESA-N ChemAxon polar_surface_area 79.11 ChemAxon refractivity 56.2 ChemAxon polarizability 21.05 ChemAxon rotatable_bond_count 3 ChemAxon acceptor_count 3 ChemAxon donor_count 3 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Nitrogen metabolism The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction and dissimilatory nitrate reduction both for conversion to ammonia, and denitrification. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere. Nitrate can be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK or a nitrate / nitrite transporter NarU. Nitrate is then reduced by a Nitrate Reductase resulting in the release of water, an acceptor and a Nitrite. Nitrite can also be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK Nitrite can be reduced a NADPH dependent nitrite reductase resulting in water and NAD and Ammonia. Nitrite can interact with hydrogen ion, ferrocytochrome c through a cytochrome c-552 ferricytochrome resulting in the release of ferricytochrome c, water and ammonia Another process by which ammonia is produced is by a reversible reaction of hydroxylamine with a reduced acceptor through a hydroxylamine reductase resulting in an acceptor, water and ammonia. Water and carbon dioxide react through a carbonate dehydratase resulting in carbamic acid. This compound reacts spontaneously with hydrogen ion resulting in the release of carbon dioxide and ammonia. Carbon dioxide can interact with water through a carbonic anhydrase resulting in hydrogen carbonate. This compound interacts with cyanate and hydrogen ion through a cyanate hydratase resulting in a carbamic acid. Ammonia can be metabolized by reacting with L-glutamine and ATP driven glutamine synthetase resulting in ADP, phosphate and L-glutamine. The latter compound reacts with oxoglutaric acid and hydrogen ion through a NADPH dependent glutamate synthase resulting in the release of NADP and L-glutamic acid. L-glutamic acid reacts with water through a NADP-specific glutamate dehydrogenase resulting in the release of oxoglutaric acid, NADPH, hydrogen ion and ammonia. PW000755 ec00910 Metabolic Phenylalanine, tyrosine and tryptophan biosynthesis ec00400 Glycine, serine and threonine metabolism ec00260 Tryptophan metabolism The biosynthesis of L-tryptophan begins with L-glutamine interacting with a chorismate through a anthranilate synthase which results in a L-glutamic acid, a pyruvic acid, a hydrogen ion and a 2-aminobenzoic acid. The aminobenzoic acid interacts with a phosphoribosyl pyrophosphate through an anthranilate synthase component II resulting in a pyrophosphate and a N-(5-phosphoribosyl)-anthranilate. The latter compound is then metabolized by an indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase resulting in a 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate. This compound then interacts with a hydrogen ion through a indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase resulting in the release of carbon dioxide, a water molecule and a (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate. The latter compound then interacts with a D-glyceraldehyde 3-phosphate and an Indole. The indole interacts with an L-serine through a tryptophan synthase, β subunit dimer resulting in a water molecule and an L-tryptophan. The metabolism of L-tryptophan starts with L-tryptophan being dehydrogenated by a tryptophanase / L-cysteine desulfhydrase resulting in the release of a hydrogen ion, an Indole and a 2-aminoacrylic acid. The latter compound is isomerized into a 2-iminopropanoate. This compound then interacts with a water molecule and a hydrogen ion spontaneously resulting in the release of an Ammonium and a pyruvic acid. The pyruvic acid then interacts with a coenzyme A through a NAD driven pyruvate dehydrogenase complex resulting in the release of a NADH, a carbon dioxide and an Acetyl-CoA PW000815 ec00380 Metabolic Aminoacyl-tRNA biosynthesis ec00970 Metabolic pathways eco01100 Trp Operon When tryptophan is lacking in the environment, the repressor is made, but it is unable to bind to the DNA operator in order to block transcription. RNA polymerase binds to the promoter site and then goes down the DNA, transcribing the genes for the tryptophan biosynthesis enzymes. PW000965 Signaling Trp Operon Inactivation When tryptophan is present in the environment, the bacteria no longer needs to make tryptophan. Therefore tryptophan binds to the repressor and activates it. The repressor then binds to the operator, located within the promoter and blocks transcription of the trp operon PW000966 Signaling 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 tryptophan metabolism II The biosynthesis of L-tryptophan begins with L-glutamine interacting with a chorismate through a anthranilate synthase which results in a L-glutamic acid, a pyruvic acid, a hydrogen ion and a 2-aminobenzoic acid. The aminobenzoic acid interacts with a phosphoribosyl pyrophosphate through an anthranilate synthase component II resulting in a pyrophosphate and a N-(5-phosphoribosyl)-anthranilate. The latter compound is then metabolized by an indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase resulting in a 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate. This compound then interacts with a hydrogen ion through a indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase resulting in the release of carbon dioxide, a water molecule and a (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate. The latter compound then interacts with a D-glyceraldehyde 3-phosphate and an Indole. The indole interacts with an L-serine through a tryptophan synthase, β subunit dimer resulting in a water molecule and an L-tryptophan. The metabolism of L-tryptophan starts with L-tryptophan being dehydrogenated by a tryptophanase / L-cysteine desulfhydrase resulting in the release of a hydrogen ion, an Indole and a 2-aminoacrylic acid. The latter compound is isomerized into a 2-iminopropanoate. This compound then interacts with a water molecule and a hydrogen ion spontaneously resulting in the release of an Ammonium and a pyruvic acid. The pyruvic acid then interacts with a coenzyme A through a NAD driven pyruvate dehydrogenase complex resulting in the release of a NADH, a carbon dioxide and an Acetyl-CoA PW001916 Metabolic tRNA charging TRNA-CHARGING-PWY tryptophan degradation II (via pyruvate) TRYPDEG-PWY tryptophan biosynthesis TRPSYN-PWY Specdb::CMs 673 Specdb::CMs 674 Specdb::CMs 675 Specdb::CMs 676 Specdb::CMs 1845 Specdb::CMs 1879 Specdb::CMs 2371 Specdb::CMs 29838 Specdb::CMs 30108 Specdb::CMs 30213 Specdb::CMs 30316 Specdb::CMs 30704 Specdb::CMs 30741 Specdb::CMs 30772 Specdb::CMs 31262 Specdb::CMs 31263 Specdb::CMs 37846 Specdb::CMs 174758 Specdb::CMs 1081790 Specdb::CMs 1081792 Specdb::CMs 1081794 Specdb::CMs 1081796 Specdb::CMs 1081797 Specdb::NmrOneD 1288 Specdb::NmrOneD 1608 Specdb::NmrOneD 8002 Specdb::NmrOneD 8003 Specdb::NmrOneD 8004 Specdb::NmrOneD 8005 Specdb::NmrOneD 8006 Specdb::NmrOneD 8007 Specdb::NmrOneD 8008 Specdb::NmrOneD 8009 Specdb::NmrOneD 8010 Specdb::NmrOneD 8011 Specdb::NmrOneD 8012 Specdb::NmrOneD 8013 Specdb::NmrOneD 8014 Specdb::NmrOneD 8015 Specdb::NmrOneD 8016 Specdb::NmrOneD 8017 Specdb::NmrOneD 8018 Specdb::NmrOneD 8019 Specdb::NmrOneD 8020 Specdb::NmrOneD 8021 Specdb::NmrOneD 166501 Specdb::MsMs 4898 Specdb::MsMs 4899 Specdb::MsMs 4900 Specdb::MsMs 4901 Specdb::MsMs 4902 Specdb::MsMs 4903 Specdb::MsMs 4904 Specdb::MsMs 4905 Specdb::MsMs 4906 Specdb::MsMs 4907 Specdb::MsMs 4908 Specdb::MsMs 4909 Specdb::MsMs 4910 Specdb::MsMs 4923 Specdb::MsMs 437026 Specdb::MsMs 437027 Specdb::MsMs 437028 Specdb::MsMs 437029 Specdb::MsMs 437030 Specdb::MsMs 438481 Specdb::MsMs 438482 Specdb::MsMs 438483 Specdb::MsMs 438484 Specdb::MsMs 438485 Specdb::MsMs 438767 Specdb::NmrTwoD 1047 Specdb::NmrTwoD 1549 HMDB00929 6305 6066 C00078 27897 TRP TRP_LFZW_DHE1 L-Tryptophan Keseler, I. 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Organic Letters (2007), 9(8), 1513-1516. http://hmdb.ca/system/metabolites/msds/000/000/836/original/HMDB00929.pdf?1358894694 Tryptophanyl-tRNA synthetase P00954 SYW_ECOLI trpS http://ecmdb.ca/proteins/P00954.xml Tryptophanase P0A853 TNAA_ECOLI tnaA http://ecmdb.ca/proteins/P0A853.xml Tryptophan synthase alpha chain P0A877 TRPA_ECOLI trpA http://ecmdb.ca/proteins/P0A877.xml Tryptophan synthase beta chain P0A879 TRPB_ECOLI trpB http://ecmdb.ca/proteins/P0A879.xml N-methyl-L-tryptophan oxidase P40874 MTOX_ECOLI solA http://ecmdb.ca/proteins/P40874.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 Tryptophan-specific transport protein P0AAD2 MTR_ECOLI mtr http://ecmdb.ca/proteins/P0AAD2.xml Aromatic amino acid transport protein AroP P15993 AROP_ECOLI aroP http://ecmdb.ca/proteins/P15993.xml Low affinity tryptophan permease P23173 TNAB_ECOLI tnaB http://ecmdb.ca/proteins/P23173.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Inner membrane protein yddG P46136 YDDG_ECOLI yddG http://ecmdb.ca/proteins/P46136.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 Indole + L-Serine > Water + L-Tryptophan R00674 RXN0-2382 Indoleglycerol phosphate + L-Serine > D-Glyceraldehyde 3-phosphate + Water + L-Tryptophan R02722 TRYPSYN-RXN N-Methyltryptophan + Water + Oxygen > Formaldehyde + Hydrogen peroxide + L-Tryptophan RXN0-301 Adenosine triphosphate + tRNA(Trp) + L-Tryptophan + tRNA(Trp) <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp) R03664 Water + L-Tryptophan <> Indole + Ammonium + Pyruvic acid L-Tryptophan + Water <> Indole + Pyruvic acid + Ammonia R00673 TRYPTOPHAN-RXN L-Serine + Indole <> L-Tryptophan + Water R00674 L-Serine + Indoleglycerol phosphate <> L-Tryptophan + D-Glyceraldehyde 3-phosphate + Water R02722 Adenosine triphosphate + L-Tryptophan + tRNA(Trp) <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp) R03664 L-Tryptophan + Water <> Hydrogen ion + Indole + Pyruvic acid + Ammonia TRYPTOPHAN-RXN N-methyl-L-tryptophan + Water + Oxygen > L-Tryptophan + Formaldehyde + Hydrogen peroxide Adenosine triphosphate + L-Tryptophan + tRNA(Trp) > Adenosine monophosphate + Pyrophosphate + L-tryptophyl-tRNA(Trp) L-Tryptophan + Water > Indole + Pyruvic acid + Ammonia L-Serine + Indoleglycerol phosphate > L-Tryptophan + glyceraldehyde 3-phosphate + Water L-Tryptophan + Water + 2-Aminoacrylic acid + 2-Iminopropanoate <> Indole + Pyruvic acid + Ammonia R00673 L-Serine + Indoleglycerol phosphate + Indole <> L-Tryptophan + D-Glyceraldehyde 3-phosphate + Water R02722 L-Tryptophan + Adenosine triphosphate + Hydrogen ion + tRNA(Trp) > Adenosine monophosphate + Pyrophosphate + L-tryptophyl-tRNA(Trp) PW_R002836 Indole + L-Serine + L-Serine > Water + L-Tryptophan PW_R002900 L-Tryptophan > Hydrogen ion + Indole + 2-Aminoacrylic acid PW_R002901 Indole + L-Serine > Water + L-Tryptophan Adenosine triphosphate + tRNA(Trp) + L-Tryptophan <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp) Indole + L-Serine > Water + L-Tryptophan L-Serine + Indole <> L-Tryptophan + Water Adenosine triphosphate + tRNA(Trp) + L-Tryptophan <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp) 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 12.1 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 48400 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 23.6 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 94400 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 20.6 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 82400 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 9.39 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 37560 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 13.57 uM true 1.23 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 54267 4937 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