2.02012-05-31 13:02:13 -06002015-09-13 12:56:09 -0600ECMDB00929M2MDB000203L-TryptophanTryptophan 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 acid1-b-3-Indolylalanine1-beta-3-Indolylalanine1-β-3-Indolylalanine1b-3-Indolylalanine1beta-3-Indolylalanine1H-Indole-3-Alanine1β-3-Indolylalanine2-Amino-3-indolylpropanate2-Amino-3-indolylpropanic acid2-Amino-3-indolylpropanoate2-Amino-3-indolylpropanoic acid3-(1H-Indol-3-yl)-L-Alanine3-Indol-3-ylalaninea-Aminoindole-3-propionatea-Aminoindole-3-propionic acidAlpha'-Amino-3-indolepropionateAlpha'-Amino-3-indolepropionic acidAlpha-Aminoindole-3-propionateAlpha-Aminoindole-3-propionic acidArdeytropinH-TRP-ohIndole-3-alanineKalmaL-(-)-TryptophanL-a-amino-3-IndolepropionateL-a-amino-3-Indolepropionic acidL-a-Aminoindole-3-propionateL-a-Aminoindole-3-propionic acidL-alpha-Amino-3-indolepropionateL-alpha-Amino-3-indolepropionic acidL-alpha-Aminoindole-3-propionateL-alpha-Aminoindole-3-propionic acidL-b-3-IndolylalanineL-beta-3-IndolylalanineL-TryptofanL-TryptophanL-TryptophaneL-α-amino-3-IndolepropionateL-α-amino-3-Indolepropionic acidL-α-Aminoindole-3-propionateL-α-Aminoindole-3-propionic acidL-β-3-IndolylalanineLopac-T-0254LyphanOptimaxPacitronSedanoctTriptofanoTrofanTrpTryptacinTryptanTryptophanTryptophaneTryptophanumWα-Aminoindole-3-propionateα-Aminoindole-3-propionic acidC11H12N2O2204.2252204.089877638(2S)-2-amino-3-(1H-indol-3-yl)propanoic acidL-tryptophan73-22-3N[C@@H](CC1=CNC2=CC=CC=C12)C(O)=OInChI=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/s1QIVBCDIJIAJPQS-VIFPVBQESA-NSolidCytosolExtra-organismPeriplasmlogp-1.10logs-2.18solubility1.36e+00 g/lmelting_point230 oClogp-1.1pka_strongest_acidic2.54pka_strongest_basic9.4iupac(2S)-2-amino-3-(1H-indol-3-yl)propanoic acidaverage_mass204.2252mono_mass204.089877638smilesN[C@@H](CC1=CNC2=CC=CC=C12)C(O)=OformulaC11H12N2O2inchiInChI=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/s1inchikeyQIVBCDIJIAJPQS-VIFPVBQESA-Npolar_surface_area79.11refractivity56.2polarizability21.05rotatable_bond_count3acceptor_count3donor_count3physiological_charge0formal_charge0Nitrogen 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.
PW000755ec00910MetabolicPhenylalanine, tyrosine and tryptophan biosynthesisec00400Glycine, serine and threonine metabolismec00260Tryptophan metabolismThe 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
PW000815ec00380MetabolicAminoacyl-tRNA biosynthesisec00970Metabolic pathwayseco01100Trp OperonWhen 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.PW000965SignalingTrp Operon InactivationWhen 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 operonPW000966Signalinginner membrane transportlist 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 addedPW000786MetabolictRNA Charging 2This pathway groups together all E. coli tRNA charging reactions.PW000803MetabolictRNA chargingThis pathway groups together all E. coli tRNA charging reactions.PW000799Metabolictryptophan metabolism IIThe 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-CoAPW001916MetabolictRNA chargingTRNA-CHARGING-PWYtryptophan degradation II (via pyruvate)TRYPDEG-PWYtryptophan biosynthesisTRPSYN-PWYSpecdb::CMs673Specdb::CMs674Specdb::CMs675Specdb::CMs676Specdb::CMs1845Specdb::CMs1879Specdb::CMs2371Specdb::CMs29838Specdb::CMs30108Specdb::CMs30213Specdb::CMs30316Specdb::CMs30704Specdb::CMs30741Specdb::CMs30772Specdb::CMs31262Specdb::CMs31263Specdb::CMs37846Specdb::CMs174758Specdb::CMs1081790Specdb::CMs1081792Specdb::CMs1081794Specdb::CMs1081796Specdb::CMs1081797Specdb::NmrOneD1288Specdb::NmrOneD1608Specdb::NmrOneD8002Specdb::NmrOneD8003Specdb::NmrOneD8004Specdb::NmrOneD8005Specdb::NmrOneD8006Specdb::NmrOneD8007Specdb::NmrOneD8008Specdb::NmrOneD8009Specdb::NmrOneD8010Specdb::NmrOneD8011Specdb::NmrOneD8012Specdb::NmrOneD8013Specdb::NmrOneD8014Specdb::NmrOneD8015Specdb::NmrOneD8016Specdb::NmrOneD8017Specdb::NmrOneD8018Specdb::NmrOneD8019Specdb::NmrOneD8020Specdb::NmrOneD8021Specdb::NmrOneD166501Specdb::MsMs4898Specdb::MsMs4899Specdb::MsMs4900Specdb::MsMs4901Specdb::MsMs4902Specdb::MsMs4903Specdb::MsMs4904Specdb::MsMs4905Specdb::MsMs4906Specdb::MsMs4907Specdb::MsMs4908Specdb::MsMs4909Specdb::MsMs4910Specdb::MsMs4923Specdb::MsMs437026Specdb::MsMs437027Specdb::MsMs437028Specdb::MsMs437029Specdb::MsMs437030Specdb::MsMs438481Specdb::MsMs438482Specdb::MsMs438483Specdb::MsMs438484Specdb::MsMs438485Specdb::MsMs438767Specdb::NmrTwoD1047Specdb::NmrTwoD1549HMDB0092963056066C0007827897TRPTRP_LFZW_DHE1L-TryptophanKeseler, I. 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Organic Letters (2007), 9(8), 1513-1516.http://hmdb.ca/system/metabolites/msds/000/000/836/original/HMDB00929.pdf?1358894694Tryptophanyl-tRNA synthetaseP00954SYW_ECOLItrpShttp://ecmdb.ca/proteins/P00954.xmlTryptophanaseP0A853TNAA_ECOLItnaAhttp://ecmdb.ca/proteins/P0A853.xmlTryptophan synthase alpha chainP0A877TRPA_ECOLItrpAhttp://ecmdb.ca/proteins/P0A877.xmlTryptophan synthase beta chainP0A879TRPB_ECOLItrpBhttp://ecmdb.ca/proteins/P0A879.xmlN-methyl-L-tryptophan oxidaseP40874MTOX_ECOLIsolAhttp://ecmdb.ca/proteins/P40874.xmlUncharacterized amino-acid ABC transporter ATP-binding protein yecCP37774YECC_ECOLIyecChttp://ecmdb.ca/proteins/P37774.xmlInner membrane amino-acid ABC transporter permease protein yecSP0AFT2YECS_ECOLIyecShttp://ecmdb.ca/proteins/P0AFT2.xmlTryptophan-specific transport proteinP0AAD2MTR_ECOLImtrhttp://ecmdb.ca/proteins/P0AAD2.xmlAromatic amino acid transport protein AroPP15993AROP_ECOLIaroPhttp://ecmdb.ca/proteins/P15993.xmlLow affinity tryptophan permeaseP23173TNAB_ECOLItnaBhttp://ecmdb.ca/proteins/P23173.xmlOuter membrane protein NP77747OMPN_ECOLIompNhttp://ecmdb.ca/proteins/P77747.xmlInner membrane protein yddGP46136YDDG_ECOLIyddGhttp://ecmdb.ca/proteins/P46136.xmlOuter membrane pore protein EP02932PHOE_ECOLIphoEhttp://ecmdb.ca/proteins/P02932.xmlOuter membrane protein FP02931OMPF_ECOLIompFhttp://ecmdb.ca/proteins/P02931.xmlOuter membrane protein CP06996OMPC_ECOLIompChttp://ecmdb.ca/proteins/P06996.xmlIndole + L-Serine > Water + L-TryptophanR00674RXN0-2382Indoleglycerol phosphate + L-Serine > D-Glyceraldehyde 3-phosphate + Water + L-TryptophanR02722TRYPSYN-RXNN-Methyltryptophan + Water + Oxygen > Formaldehyde + Hydrogen peroxide + L-TryptophanRXN0-301Adenosine triphosphate + tRNA(Trp) + L-Tryptophan + tRNA(Trp) <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp)R03664Water + L-Tryptophan <> Indole + Ammonium + Pyruvic acidL-Tryptophan + Water <> Indole + Pyruvic acid + AmmoniaR00673TRYPTOPHAN-RXNL-Serine + Indole <> L-Tryptophan + WaterR00674L-Serine + Indoleglycerol phosphate <> L-Tryptophan + D-Glyceraldehyde 3-phosphate + WaterR02722Adenosine triphosphate + L-Tryptophan + tRNA(Trp) <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp)R03664L-Tryptophan + Water <> Hydrogen ion + Indole + Pyruvic acid + AmmoniaTRYPTOPHAN-RXNN-methyl-L-tryptophan + Water + Oxygen > L-Tryptophan + Formaldehyde + Hydrogen peroxideAdenosine triphosphate + L-Tryptophan + tRNA(Trp) > Adenosine monophosphate + Pyrophosphate + L-tryptophyl-tRNA(Trp)L-Tryptophan + Water > Indole + Pyruvic acid + AmmoniaL-Serine + Indoleglycerol phosphate > L-Tryptophan + glyceraldehyde 3-phosphate + WaterL-Tryptophan + Water + 2-Aminoacrylic acid + 2-Iminopropanoate <> Indole + Pyruvic acid + AmmoniaR00673 L-Serine + Indoleglycerol phosphate + Indole <> L-Tryptophan + D-Glyceraldehyde 3-phosphate + WaterR02722 L-Tryptophan + Adenosine triphosphate + Hydrogen ion + tRNA(Trp) > Adenosine monophosphate + Pyrophosphate + L-tryptophyl-tRNA(Trp)PW_R002836Indole + L-Serine + L-Serine > Water + L-TryptophanPW_R002900L-Tryptophan > Hydrogen ion + Indole + 2-Aminoacrylic acidPW_R002901Indole + L-Serine > Water + L-TryptophanAdenosine triphosphate + tRNA(Trp) + L-Tryptophan <> Adenosine monophosphate + Pyrophosphate + L-Tryptophanyl-tRNA(Trp)Indole + L-Serine > Water + L-TryptophanL-Serine + Indole <> L-Tryptophan + WaterAdenosine 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 glucoseShake flask and filter culture12.1uM0.037 oCK12 NCM3722Mid-Log Phase484000Bennett, 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 5:593-599.19561621Gutnick 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 glycerolShake flask and filter culture23.6uM0.037 oCK12 NCM3722Mid-Log Phase944000Bennett, 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 5:593-599.19561621Gutnick 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 acetateShake flask and filter culture20.6uM0.037 oCK12 NCM3722Mid-Log Phase824000Bennett, 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 5:593-599.1956162148 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 GlucoBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h9.39uM0.037 oCBW25113Stationary Phase, glucose limited375600Ishii, 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." 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