2.02012-05-31 13:00:55 -06002015-09-13 12:56:09 -0600ECMDB00738M2MDB000181IndoleIndole is an aromatic heterocyclic organic compound. It has a bicyclic structure, consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. It can be produced by bacteria as a degradation product of the amino acid tryptophan. It occurs naturally in feces and has an intense fecal smell. At very low concentrations, however, it has a flowery smell, and is a constituent of many flower scents (such as orange blossoms) and perfumes. Natural jasmine oil, used in the perfume industry, contains around 2.5% of indole. Indole also occurs in CoAl tar. The participation of the nitrogen lone electron pair in the aromatic ring means that indole is not a base, and it does not behave like a simple amine.1-Azaindene1-Benzazole2,3-BenzopyrroleBenzo[b]pyrroleIndoleKetoleC8H7N117.1479117.0578492291H-indoleindole120-72-9N1C=CC2=C1C=CC=C2InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9HSIKJAQJRHWYJAI-UHFFFAOYSA-NSolidCytosolExtra-organismMembranePeriplasmlogp2.29logs-1.34solubility5.31e+00 g/lmelting_point52.5 oClogp2.07pka_strongest_acidic16.44iupac1H-indoleaverage_mass117.1479mono_mass117.057849229smilesN1C=CC2=C1C=CC=C2formulaC8H7NinchiInChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9HinchikeySIKJAQJRHWYJAI-UHFFFAOYSA-Npolar_surface_area15.79refractivity37.14polarizability12.82rotatable_bond_count0acceptor_count0donor_count1physiological_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
PW000815ec00380MetabolicMetabolic pathwayseco01100tryptophan 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-CoAPW001916Metabolictryptophan degradation II (via pyruvate)TRYPDEG-PWYtryptophan biosynthesisTRPSYN-PWYSpecdb::CMs2683Specdb::CMs27171Specdb::CMs27342Specdb::CMs27536Specdb::CMs99600Specdb::CMs99601Specdb::CMs99602Specdb::CMs148814Specdb::EiMs319Specdb::NmrOneD1511Specdb::NmrOneD2184Specdb::NmrOneD2875Specdb::NmrOneD5138Specdb::NmrOneD5139Specdb::MsMs1047Specdb::MsMs1048Specdb::MsMs1049Specdb::MsMs4590Specdb::MsMs4591Specdb::MsMs4592Specdb::MsMs4593Specdb::MsMs182706Specdb::MsMs182707Specdb::MsMs182708Specdb::MsMs183054Specdb::MsMs183055Specdb::MsMs183056Specdb::MsMs447947Specdb::MsMs448373Specdb::MsMs448374Specdb::MsMs448375Specdb::MsMs448376Specdb::MsMs448377Specdb::MsMs448378Specdb::MsMs448379Specdb::MsMs448380Specdb::MsMs448381Specdb::MsMs448382Specdb::MsMs448383Specdb::NmrTwoD1035Specdb::NmrTwoD1457HMDB00738798776C0046316881INDOLEINDIndoleKeseler, 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-D590.21097882Kanehisa, 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-D114.22080510van 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 370:17-25.17765195Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). 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(1973), 6 pp. http://hmdb.ca/system/metabolites/msds/000/000/657/original/HMDB00738.pdf?1358894583TryptophanaseP0A853TNAA_ECOLItnaAhttp://ecmdb.ca/proteins/P0A853.xmlTryptophan synthase alpha chainP0A877TRPA_ECOLItrpAhttp://ecmdb.ca/proteins/P0A877.xmlTryptophan synthase beta chainP0A879TRPB_ECOLItrpBhttp://ecmdb.ca/proteins/P0A879.xmlTryptophan-specific transport proteinP0AAD2MTR_ECOLImtrhttp://ecmdb.ca/proteins/P0AAD2.xmlOuter membrane protein NP77747OMPN_ECOLIompNhttp://ecmdb.ca/proteins/P77747.xmlOuter membrane pore protein EP02932PHOE_ECOLIphoEhttp://ecmdb.ca/proteins/P02932.xmlOuter membrane protein FP02931OMPF_ECOLIompFhttp://ecmdb.ca/proteins/P02931.xmlAcriflavine resistance protein FP24181ACRF_ECOLIacrFhttp://ecmdb.ca/proteins/P24181.xmlOuter membrane protein tolCP02930TOLC_ECOLItolChttp://ecmdb.ca/proteins/P02930.xmlAcriflavine resistance protein EP24180ACRE_ECOLIacrEhttp://ecmdb.ca/proteins/P24180.xmlOuter membrane protein CP06996OMPC_ECOLIompChttp://ecmdb.ca/proteins/P06996.xmlIndole + L-Serine > Water + L-TryptophanR00674RXN0-2382Indoleglycerol phosphate > D-Glyceraldehyde 3-phosphate + IndoleR02340RXN0-2381Water + L-Tryptophan <> Indole + Ammonium + Pyruvic acidL-Tryptophan + Water <> Indole + Pyruvic acid + AmmoniaR00673TRYPTOPHAN-RXNL-Serine + Indole <> L-Tryptophan + WaterR00674Indoleglycerol phosphate <> Indole + D-Glyceraldehyde 3-phosphateR02340L-Tryptophan + Water <> Hydrogen ion + Indole + Pyruvic acid + AmmoniaTRYPTOPHAN-RXNL-Tryptophan + Water > Indole + Pyruvic acid + AmmoniaL-Tryptophan + Water + 2-Aminoacrylic acid + 2-Iminopropanoate <> Indole + Pyruvic acid + AmmoniaR00673 L-Serine + Indoleglycerol phosphate + Indole <> L-Tryptophan + D-Glyceraldehyde 3-phosphate + WaterR02722 (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate > D-Glyceraldehyde 3-phosphate + Indole + D-Glyceraldehyde 3-phosphatePW_R002899Indole + L-Serine + L-Serine > Water + L-TryptophanPW_R002900L-Tryptophan > Hydrogen ion + Indole + 2-Aminoacrylic acidPW_R002901Indole + L-Serine > Water + L-TryptophanIndole + L-Serine > Water + L-TryptophanL-Serine + Indole <> L-Tryptophan + Water