2.0 2012-05-31 10:23:49 -0600 2015-09-13 12:56:07 -0600 ECMDB00214 M2MDB000087 Ornithine Ornithine 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. &alpha;,&delta;-diaminovalerate &alpha;,&delta;-diaminovaleric acid (+)-S-Ornithine (S)-2,5-Diaminopentanoate (S)-2,5-Diaminopentanoic acid (S)-a,D-Diaminovalerate (S)-a,D-Diaminovaleric acid (S)-Ornithine 2, 5-Diaminopentanoate 2, 5-Diaminopentanoic acid 2, 5-Diaminovalerate 2, 5-Diaminovaleric acid 5-Amino-L-Norvaline a,delta-Diaminovalerate a,delta-Diaminovaleric acid a,δ-Diaminovalerate a,δ-Diaminovaleric acid Alpha,delta-Diaminovalerate Alpha,delta-Diaminovaleric acid L-(-)-Ornithine L-Ornithine Ornithine α,δ-Diaminovalerate α,δ-Diaminovaleric acid C5H12N2O2 132.161 132.089877638 (2S)-2,5-diaminopentanoic acid ornithine 70-26-8 NCCC[C@H](N)C(O)=O InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1 AHLPHDHHMVZTML-BYPYZUCNSA-N Solid Cytosol Extra-organism Periplasm logp -3.64 ALOGPS logs 0.11 ALOGPS solubility 1.72e+02 g/l ALOGPS melting_point 140 oC logp -3.7 ChemAxon pka_strongest_acidic 2.67 ChemAxon pka_strongest_basic 10.29 ChemAxon iupac (2S)-2,5-diaminopentanoic acid ChemAxon average_mass 132.161 ChemAxon mono_mass 132.089877638 ChemAxon smiles NCCC[C@H](N)C(O)=O ChemAxon formula C5H12N2O2 ChemAxon inchi InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1 ChemAxon inchikey AHLPHDHHMVZTML-BYPYZUCNSA-N ChemAxon polar_surface_area 89.34 ChemAxon refractivity 33.21 ChemAxon polarizability 13.85 ChemAxon rotatable_bond_count 4 ChemAxon acceptor_count 4 ChemAxon donor_count 3 ChemAxon physiological_charge 1 ChemAxon formal_charge 0 ChemAxon Glutathione metabolism The 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. PW000833 ec00480 Metabolic Arginine and proline metabolism ec00330 ABC transporters ec02010 arginine metabolism The 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 cycle PW000790 Metabolic ornithine 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. PW000791 Metabolic ornithine biosynthesis GLUTORN-PWY arginine biosynthesis I ARGSYN-PWY putrescine biosynthesis III PWY-46 superpathway of ornithine degradation ORNDEG-PWY Specdb::CMs 472 Specdb::CMs 473 Specdb::CMs 474 Specdb::CMs 1291 Specdb::CMs 1415 Specdb::CMs 1484 Specdb::CMs 1750 Specdb::CMs 2994 Specdb::CMs 30085 Specdb::CMs 30379 Specdb::CMs 30606 Specdb::CMs 30798 Specdb::CMs 31079 Specdb::CMs 31080 Specdb::CMs 31081 Specdb::CMs 31082 Specdb::CMs 31791 Specdb::CMs 32270 Specdb::CMs 32271 Specdb::CMs 32273 Specdb::CMs 37363 Specdb::CMs 130647 Specdb::CMs 138381 Specdb::CMs 1054761 Specdb::CMs 1054763 Specdb::NmrOneD 1206 Specdb::NmrOneD 1207 Specdb::NmrOneD 4859 Specdb::NmrOneD 6152 Specdb::NmrOneD 6153 Specdb::NmrOneD 6154 Specdb::NmrOneD 6155 Specdb::NmrOneD 6156 Specdb::NmrOneD 6157 Specdb::NmrOneD 6158 Specdb::NmrOneD 6159 Specdb::NmrOneD 6160 Specdb::NmrOneD 6161 Specdb::NmrOneD 6162 Specdb::NmrOneD 6163 Specdb::NmrOneD 6164 Specdb::NmrOneD 6165 Specdb::NmrOneD 6166 Specdb::NmrOneD 6167 Specdb::NmrOneD 6168 Specdb::NmrOneD 6169 Specdb::NmrOneD 6170 Specdb::NmrOneD 6171 Specdb::NmrOneD 166442 Specdb::MsMs 349 Specdb::MsMs 350 Specdb::MsMs 351 Specdb::MsMs 3635 Specdb::MsMs 3636 Specdb::MsMs 3637 Specdb::MsMs 3638 Specdb::MsMs 3639 Specdb::MsMs 3640 Specdb::MsMs 3641 Specdb::MsMs 3642 Specdb::MsMs 3643 Specdb::MsMs 3644 Specdb::MsMs 3645 Specdb::MsMs 3646 Specdb::MsMs 3647 Specdb::MsMs 3648 Specdb::MsMs 3649 Specdb::MsMs 3650 Specdb::MsMs 3651 Specdb::MsMs 3652 Specdb::MsMs 3653 Specdb::MsMs 179271 Specdb::MsMs 179272 Specdb::MsMs 179273 Specdb::NmrTwoD 996 Specdb::NmrTwoD 1212 HMDB00214 6262 6026 C01602 L-ORNITHINE ORN Ornithine Keseler, I. 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Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 8pp. http://hmdb.ca/system/metabolites/msds/000/000/152/original/HMDB00214.pdf?1358463180 Ornithine carbamoyltransferase chain I P04391 OTC1_ECOLI argI http://ecmdb.ca/proteins/P04391.xml Ornithine carbamoyltransferase chain F P06960 OTC2_ECOLI argF http://ecmdb.ca/proteins/P06960.xml Histidine transport ATP-binding protein hisP P07109 HISP_ECOLI hisP http://ecmdb.ca/proteins/P07109.xml Ornithine decarboxylase, constitutive P21169 DCOR_ECOLI speC http://ecmdb.ca/proteins/P21169.xml Acetylornithine deacetylase P23908 ARGE_ECOLI argE http://ecmdb.ca/proteins/P23908.xml Ornithine decarboxylase, inducible P24169 DCOS_ECOLI speF http://ecmdb.ca/proteins/P24169.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 Histidine transport ATP-binding protein hisP P07109 HISP_ECOLI hisP http://ecmdb.ca/proteins/P07109.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 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 Putative arginine/ornithine antiporter P0AAE5 ARCD_ECOLI ydgI http://ecmdb.ca/proteins/P0AAE5.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Putrescine-ornithine antiporter P0AAF1 POTE_ECOLI potE http://ecmdb.ca/proteins/P0AAF1.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml Adenosine triphosphate + Water + Ornithine > ADP + Hydrogen ion + Ornithine + Phosphate ABC-37-RXN Adenosine triphosphate + Water + Ornithine > ADP + Hydrogen ion + Ornithine + Phosphate ABC-37-RXN Hydrogen ion + Ornithine + L-Ornithine <> Carbon dioxide + Putrescine + Ethylenediamine R00670 ORNDECARBOX-RXN Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + Phosphate R01398 ORNCARBAMTRANSFER-RXN N-Acetylornithine + Water <> Acetic acid + Ornithine + L-Ornithine R00669 ACETYLORNDEACET-RXN N-Acetylornithine + Water <> Acetic acid + Ornithine R00669 Ornithine <> Putrescine + Carbon dioxide R00670 Carbamoylphosphate + Ornithine <> Phosphate + Citrulline R01398 Adenosine triphosphate + Ornithine + Water > ADP + Phosphate + Ornithine + Hydrogen ion ABC-37-RXN Adenosine triphosphate + Ornithine + Water > ADP + Phosphate + Ornithine + Hydrogen ion ABC-37-RXN N-Acetylornithine + Water > Ornithine + Acetic acid ACETYLORNDEACET-RXN Ornithine + Carbamoylphosphate <> Hydrogen ion + Citrulline + Phosphate R01398 ORNCARBAMTRANSFER-RXN Hydrogen ion + Ornithine > Carbon dioxide + Putrescine ORNDECARBOX-RXN Ornithine > Putrescine + Carbon dioxide Carbamoylphosphate + Ornithine > Inorganic phosphate + Citrulline N-Acetylornithine + Water > Ornithine + Acetic acid + Ornithine PW_R002694 Ornithine + Carbamoylphosphate + Ornithine > Phosphate + Hydrogen ion + Citrulline PW_R002676 Ornithine + Hydrogen ion + Ornithine > Putrescine + Carbon dioxide PW_R002695 Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + Phosphate Hydrogen ion + Ornithine + L-Ornithine <> Carbon dioxide + Putrescine + Ethylenediamine Ornithine <> Putrescine + Carbon dioxide N-Acetylornithine + Water <> Acetic acid + Ornithine + L-Ornithine N-Acetylornithine + Water <> Acetic acid + Ornithine + L-Ornithine 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 10.1 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 40400 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 30.3 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 121200 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 27.5 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 110000 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 120.0 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 480000 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 267.33 uM true 10.21 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 1069333 40857 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