2.02012-05-31 10:23:49 -06002015-09-13 12:56:07 -0600ECMDB00214M2MDB000087OrnithineOrnithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. It is a central part of the urea cycle, which allows for the disposal of excess nitrogen. L-Ornithine is also a precursor of citrulline and arginine.α,δ-diaminovalerateα,δ-diaminovaleric acid(+)-S-Ornithine(S)-2,5-Diaminopentanoate(S)-2,5-Diaminopentanoic acid(S)-a,D-Diaminovalerate(S)-a,D-Diaminovaleric acid(S)-Ornithine2, 5-Diaminopentanoate2, 5-Diaminopentanoic acid2, 5-Diaminovalerate2, 5-Diaminovaleric acid5-Amino-L-Norvalinea,delta-Diaminovaleratea,delta-Diaminovaleric acida,δ-Diaminovaleratea,δ-Diaminovaleric acidAlpha,delta-DiaminovalerateAlpha,delta-Diaminovaleric acidL-(-)-OrnithineL-OrnithineOrnithineα,δ-Diaminovalerateα,δ-Diaminovaleric acidC5H12N2O2132.161132.089877638(2S)-2,5-diaminopentanoic acidornithine70-26-8NCCC[C@H](N)C(O)=OInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1AHLPHDHHMVZTML-BYPYZUCNSA-NSolidCytosolExtra-organismPeriplasmlogp-3.64logs0.11solubility1.72e+02 g/lmelting_point140 oClogp-3.7pka_strongest_acidic2.67pka_strongest_basic10.29iupac(2S)-2,5-diaminopentanoic acidaverage_mass132.161mono_mass132.089877638smilesNCCC[C@H](N)C(O)=OformulaC5H12N2O2inchiInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1inchikeyAHLPHDHHMVZTML-BYPYZUCNSA-Npolar_surface_area89.34refractivity33.21polarizability13.85rotatable_bond_count4acceptor_count4donor_count3physiological_charge1formal_charge0Glutathione metabolismThe biosynthesis of glutathione starts with the introduction of L-glutamic acid through either a glutamate:sodium symporter, glutamate / aspartate : H+ symporter GltP or a
glutamate / aspartate ABC transporter. Once in the cytoplasm, L-glutamice acid reacts with L-cysteine through an ATP glutamate-cysteine ligase resulting in gamma-glutamylcysteine. This compound reacts which Glycine through an ATP driven glutathione synthetase thus catabolizing Glutathione.
This compound is metabolized through a spontaneous reaction with an oxidized glutaredoxin resulting in a reduced glutaredoxin and an oxidized glutathione. This compound is reduced by a NADPH glutathione reductase resulting in a glutathione.
PW000833ec00480MetabolicArginine and proline metabolismec00330ABC transportersec02010arginine metabolismThe metabolism of L-arginine starts with the acetylation of L-glutamic acid resulting in a N-acetylglutamic acid while releasing a coenzyme A and a hydrogen ion. N-acetylglutamic acid is then phosphorylated via an ATP driven acetylglutamate kinase which yields a N-acetyl-L-glutamyl 5-phosphate. This compound undergoes a NDPH dependent reduction resulting in N-acetyl-L-glutamate 5-semialdehyde. This compound reacts with L-glutamic acid through a acetylornithine aminotransferase / N-succinyldiaminopimelate aminotransferase to produce a N-acetylornithine which is then deacetylated through a acetylornithine deacetylase which yield an ornithine.
L-glutamine is used to synthesize carbamoyl phosphate through the interaction of L-glutamine, water, ATP, and hydrogen carbonate. This reaction yields ADP, L-glutamic acid, phosphate, and hydrogen ion.
Carbamoyl phosphate and ornithine are used to catalyze the production of citrulline through an ornithine carbamoyltransferase. Citrulline reacts with L-aspartic acid through an ATP dependent enzyme, argininosuccinate synthase to produce pyrophosphate, AMP and argininosuccinic acid. Argininosussinic acid is then lyase to produce L-arginine and fumaric acid.
L-arginine can be metabolized into succinic acid by two different sets of reactions:
1. Arginine reacts with succinyl-CoA through a arginine N-succinyltransferase resulting in N2-succinyl-L-arginine while releasing CoA and Hydrogen Ion. N2-succinyl-L-arginine is then dihydrolase to produce a N2-succinyl-L-ornithine through a N-succinylarginine dihydrolase. This compound in turn reacts with oxoglutaric acid through succinylornithine transaminase resulting in L-glutamic acid and N2-succinyl-L-glutamic acid 5-semialdehyde. This compoud in turn reacts with a NAD dependent dehydrogenase resulting in N2-succinylglutamate while releasing NADH and hydrogen ion. N2-succinylglutamate reacts with water through a succinylglutamate desuccinylase resulting in L-glutamic acid and
a succinic acid. The succinic acid is then incorporated in the TCA cycle
2.Argine reacts with carbon dioxide and a hydrogen ion through a biodegradative arginine decarboxylase, resulting in Agmatine. This compound is then transformed into putrescine by reacting with water and an agmatinase, and releasing urea. Putrescine can be metabolized by reaction with either l-glutamic acid or oxoglutaric acid. If putrescine reacts with L-glutamic acid, it reacts through an ATP mediated gamma-glutamylputrescine producing a hydrogen ion, ADP, phosphate and gamma-glutamyl-L-putrescine. This compound is reduced by interacting with oxygen, water and a gamma-glutamylputrescine oxidoreductase resulting in ammonium, hydrogen peroxide and 4-gamma-glutamylamino butanal. This compound is dehydrogenated through a NADP mediated reaction lead by gamma-glutamyl-gamma-aminobutaryaldehyde dehydrogenase resulting in hydrogen ion, NADPH and 4-glutamylamino butanoate. In turn, the latter compound reacts with water through a gamma-glutamyl-gamma-aminobutyrate hydrolase resulting in L-glutamic acid and Gamma aminobutyric acid. On the other hand, if putrescine reacts with oxoglutaric acid through a putrescine aminotransferase, it results in L-glutamic acid, and a 4-aminobutyraldehyde. This compound reacts with water through a NAD dependent gamma aminobutyraldehyde dehydrogenase resulting in hydrogen ion, NADH and gamma-aminobutyric acid.
Gamma Aaminobutyric acid reacts with oxoglutaric acid through 4-aminobutyrate aminotransferase resulting in L-glutamic acid and succinic acid semialdehyde. This compound in turn can react with with either NADP or NAD to result in the production of succinic acid through succinate-semialdehyde dehydrogenase or aldehyde dehydrogenase-like protein yneI respectively. Succinic acid can then be integrated in the TCA cycle.
L-arginine is eventua lly metabolized into succinic acid which then goes to the TCA cyclePW000790Metabolicornithine metabolism
In the ornithine biosynthesis pathway of E. coli, L-glutamate is acetylated to N-acetylglutamate by the enzyme N-acetylglutamate synthase, encoded by the argA gene. The acetyl donor for this reaction is acetyl-CoA. N-acetylglutamic acid is then phosphorylated via an ATP driven acetylglutamate kinase which yields a N-acetyl-L-glutamyl 5-phosphate. This compound undergoes a NADPH dependent reduction resulting in N-acetyl-L-glutamate 5-semialdehyde. This compound reacts with L-glutamic acid through a acetylornithine aminotransferase / N-succinyldiaminopimelate aminotransferase to produce a N-acetylornithine which is then deacetylated through a acetylornithine deacetylase which yield an ornithine. Ornithine interacts with hydrogen ion through a Ornithine decarboxylase resulting in a carbon dioxide release and a putrescine
Putrescine can be metabolized by reaction with either l-glutamic acid or oxoglutaric acid. If putrescine reacts with L-glutamic acid, it reacts through an ATP mediated gamma-glutamylputrescine producing a hydrogen ion, ADP, phosphate and gamma-glutamyl-L-putrescine. This compound is reduced by interacting with oxygen, water and a gamma-glutamylputrescine oxidoreductase resulting in ammonium, hydrogen peroxide and 4-gamma-glutamylamino butanal. This compound is dehydrogenated through a NADP mediated reaction lead by gamma-glutamyl-gamma-aminobutaryaldehyde dehydrogenase resulting in hydrogen ion, NADPH and 4-glutamylamino butanoate. In turn, the latter compound reacts with water through a gamma-glutamyl-gamma-aminobutyrate hydrolase resulting in L-glutamic acid and Gamma aminobutyric acid. On the other hand, if putrescine reacts with oxoglutaric acid through a putrescine aminotransferase, it results in L-glutamic acid, and a 4-aminobutyraldehyde. This compound reacts with water through a NAD dependent gamma aminobutyraldehyde dehydrogenase resulting in hydrogen ion, NADH and gamma-aminobutyric acid.
Gamma Aaminobutyric acid reacts with oxoglutaric acid through 4-aminobutyrate aminotransferase resulting in L-glutamic acid and succinic acid semialdehyde. This compound in turn can react with with either NADP or NAD to result in the production of succinic acid through succinate-semialdehyde dehydrogenase or aldehyde dehydrogenase-like protein yneI respectively. Succinic acid can then be integrated in the TCA cycle.
PW000791Metabolicornithine biosynthesisGLUTORN-PWYarginine biosynthesis IARGSYN-PWYputrescine biosynthesis IIIPWY-46superpathway of ornithine degradationORNDEG-PWYSpecdb::CMs472Specdb::CMs473Specdb::CMs474Specdb::CMs1291Specdb::CMs1415Specdb::CMs1484Specdb::CMs1750Specdb::CMs2994Specdb::CMs30085Specdb::CMs30379Specdb::CMs30606Specdb::CMs30798Specdb::CMs31079Specdb::CMs31080Specdb::CMs31081Specdb::CMs31082Specdb::CMs31791Specdb::CMs32270Specdb::CMs32271Specdb::CMs32273Specdb::CMs37363Specdb::CMs130647Specdb::CMs138381Specdb::CMs1054761Specdb::CMs1054763Specdb::NmrOneD1206Specdb::NmrOneD1207Specdb::NmrOneD4859Specdb::NmrOneD6152Specdb::NmrOneD6153Specdb::NmrOneD6154Specdb::NmrOneD6155Specdb::NmrOneD6156Specdb::NmrOneD6157Specdb::NmrOneD6158Specdb::NmrOneD6159Specdb::NmrOneD6160Specdb::NmrOneD6161Specdb::NmrOneD6162Specdb::NmrOneD6163Specdb::NmrOneD6164Specdb::NmrOneD6165Specdb::NmrOneD6166Specdb::NmrOneD6167Specdb::NmrOneD6168Specdb::NmrOneD6169Specdb::NmrOneD6170Specdb::NmrOneD6171Specdb::NmrOneD166442Specdb::MsMs349Specdb::MsMs350Specdb::MsMs351Specdb::MsMs3635Specdb::MsMs3636Specdb::MsMs3637Specdb::MsMs3638Specdb::MsMs3639Specdb::MsMs3640Specdb::MsMs3641Specdb::MsMs3642Specdb::MsMs3643Specdb::MsMs3644Specdb::MsMs3645Specdb::MsMs3646Specdb::MsMs3647Specdb::MsMs3648Specdb::MsMs3649Specdb::MsMs3650Specdb::MsMs3651Specdb::MsMs3652Specdb::MsMs3653Specdb::MsMs179271Specdb::MsMs179272Specdb::MsMs179273Specdb::NmrTwoD996Specdb::NmrTwoD1212HMDB0021462626026C01602L-ORNITHINEORNOrnithineKeseler, I. 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Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 8pp.http://hmdb.ca/system/metabolites/msds/000/000/152/original/HMDB00214.pdf?1358463180Ornithine carbamoyltransferase chain IP04391OTC1_ECOLIargIhttp://ecmdb.ca/proteins/P04391.xmlOrnithine carbamoyltransferase chain FP06960OTC2_ECOLIargFhttp://ecmdb.ca/proteins/P06960.xmlHistidine transport ATP-binding protein hisPP07109HISP_ECOLIhisPhttp://ecmdb.ca/proteins/P07109.xmlOrnithine decarboxylase, constitutiveP21169DCOR_ECOLIspeChttp://ecmdb.ca/proteins/P21169.xmlAcetylornithine deacetylaseP23908ARGE_ECOLIargEhttp://ecmdb.ca/proteins/P23908.xmlOrnithine decarboxylase, inducibleP24169DCOS_ECOLIspeFhttp://ecmdb.ca/proteins/P24169.xmlHistidine transport system permease protein hisMP0AEU3HISM_ECOLIhisMhttp://ecmdb.ca/proteins/P0AEU3.xmlHistidine transport system permease protein hisQP52094HISQ_ECOLIhisQhttp://ecmdb.ca/proteins/P52094.xmlLysine-arginine-ornithine-binding periplasmic proteinP09551ARGT_ECOLIargThttp://ecmdb.ca/proteins/P09551.xmlHistidine transport ATP-binding protein hisPP07109HISP_ECOLIhisPhttp://ecmdb.ca/proteins/P07109.xmlHistidine transport system permease protein hisMP0AEU3HISM_ECOLIhisMhttp://ecmdb.ca/proteins/P0AEU3.xmlHistidine transport system permease protein hisQP52094HISQ_ECOLIhisQhttp://ecmdb.ca/proteins/P52094.xmlLysine-arginine-ornithine-binding periplasmic proteinP09551ARGT_ECOLIargThttp://ecmdb.ca/proteins/P09551.xmlOuter membrane protein NP77747OMPN_ECOLIompNhttp://ecmdb.ca/proteins/P77747.xmlOuter membrane pore protein EP02932PHOE_ECOLIphoEhttp://ecmdb.ca/proteins/P02932.xmlPutative arginine/ornithine antiporterP0AAE5ARCD_ECOLIydgIhttp://ecmdb.ca/proteins/P0AAE5.xmlOuter membrane protein FP02931OMPF_ECOLIompFhttp://ecmdb.ca/proteins/P02931.xmlPutrescine-ornithine antiporterP0AAF1POTE_ECOLIpotEhttp://ecmdb.ca/proteins/P0AAF1.xmlOuter membrane protein CP06996OMPC_ECOLIompChttp://ecmdb.ca/proteins/P06996.xmlAdenosine triphosphate + Water + Ornithine > ADP + Hydrogen ion + Ornithine + PhosphateABC-37-RXNAdenosine triphosphate + Water + Ornithine > ADP + Hydrogen ion + Ornithine + PhosphateABC-37-RXNHydrogen ion + Ornithine + L-Ornithine <> Carbon dioxide + Putrescine + EthylenediamineR00670ORNDECARBOX-RXNCarbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + PhosphateR01398ORNCARBAMTRANSFER-RXNN-Acetylornithine + Water <> Acetic acid + Ornithine + L-OrnithineR00669ACETYLORNDEACET-RXNN-Acetylornithine + Water <> Acetic acid + OrnithineR00669Ornithine <> Putrescine + Carbon dioxideR00670Carbamoylphosphate + Ornithine <> Phosphate + CitrullineR01398Adenosine triphosphate + Ornithine + Water > ADP + Phosphate + Ornithine + Hydrogen ionABC-37-RXNAdenosine triphosphate + Ornithine + Water > ADP + Phosphate + Ornithine + Hydrogen ionABC-37-RXNN-Acetylornithine + Water > Ornithine + Acetic acidACETYLORNDEACET-RXNOrnithine + Carbamoylphosphate <> Hydrogen ion + Citrulline + PhosphateR01398ORNCARBAMTRANSFER-RXNHydrogen ion + Ornithine > Carbon dioxide + PutrescineORNDECARBOX-RXNOrnithine > Putrescine + Carbon dioxideCarbamoylphosphate + Ornithine > Inorganic phosphate + CitrullineN-Acetylornithine + Water > Ornithine + Acetic acid + OrnithinePW_R002694Ornithine + Carbamoylphosphate + Ornithine > Phosphate + Hydrogen ion + CitrullinePW_R002676Ornithine + Hydrogen ion + Ornithine > Putrescine + Carbon dioxidePW_R002695Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + PhosphateHydrogen ion + Ornithine + L-Ornithine <> Carbon dioxide + Putrescine + EthylenediamineOrnithine <> Putrescine + Carbon dioxideN-Acetylornithine + Water <> Acetic acid + Ornithine + L-OrnithineN-Acetylornithine + Water <> Acetic acid + Ornithine + L-OrnithineGutnick 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 culture10.1uM0.037 oCK12 NCM3722Mid-Log Phase404000Bennett, 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 culture30.3uM0.037 oCK12 NCM3722Mid-Log Phase1212000Bennett, 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 culture27.5uM0.037 oCK12 NCM3722Mid-Log Phase1100000Bennett, 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/h120.0uM0.037 oCBW25113Stationary Phase, glucose limited4800000Ishii, 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 316:593-597.17379776Luria-Bertani (LB) mediaShake flask267.33uMtrue10.2137 oCBL21 DE3Stationary phase cultures (overnight culture)106933340857Lin, 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