2.0 2012-05-31 13:01:55 -0600 2015-09-13 12:56:09 -0600 ECMDB00904 M2MDB000198 Citrulline Citrulline is an amino acid made from ornithine and carbamoyl phosphate in one of the central reactions in the urea cycle. It is also produced from arginine as a by-product of the reaction catalyzed by NOS family (NOS; EC 1.14.13.39). In this reaction arginine is first oxidized into N-hydroxyl-arginine, which is then further oxidized to citrulline concomitant with the release of nitric oxide.; EC 1.14.13.39). Citrulline's name is derived from citrullus, the Latin word for watermelon, from which it was first isolated. α-amino-γ-ureidovalerate α-amino-γ-ureidovaleric acid γureidonorvaline (2S)-2-amino-5-(carbamoylamino)pentanoate (2S)-2-amino-5-(carbamoylamino)pentanoic acid (S)-2-amino-5-(aminocarbonyl)aminopentanoate (S)-2-amino-5-(aminocarbonyl)aminopentanoic acid (S)-2-Amino-5-ureidopentanoate (S)-2-Amino-5-ureidopentanoic acid 2-Amino-5-uredovalerate 2-Amino-5-uredovaleric acid 2-Amino-5-ureidovalerate 2-Amino-5-ureidovaleric acid A-Amino-D-ureidovalerate A-Amino-D-ureidovaleric acid a-amino-delta-Ureidovalerate a-amino-delta-Ureidovaleric acid a-amino-g-Ureidovalerate a-amino-g-Ureidovaleric acid a-amino-δ-Ureidovalerate a-amino-δ-Ureidovaleric acid Alpha-Amino-delta-ureidovalerate Alpha-Amino-delta-ureidovaleric acid Alpha-Amino-gamma-ureidovalerate Alpha-Amino-gamma-ureidovaleric acid Amino-ureidovalerate Amino-ureidovaleric acid CIR CIT Citrulline Cytrulline D-Ureidonorvaline Delta-Ureidonorvaline DL-citrulline Gammaureidonorvaline H-Cit-oh L(+)-2-Amino-5-ureidovalerate L(+)-2-Amino-5-ureidovaleric acid L(+)-Citrulline L-2-Amino-5-ureido-valerate L-2-Amino-5-ureido-valeric acid L-2-Amino-5-ureidovalerate L-2-Amino-5-ureidovaleric acid L-Citrulline L-Cytrulline L-N5-carbamoyl-Ornithine Nγ-carbamylornithine N()-Carbamylornithine N(5)-(Aminocarbonyl)-DL-Ornithine N(delta)-Carbamylornithine N(δ)-Carbamylornithine N-Carbamylornithine N5-(Aminocarbonyl)-L-ornithine N5-(aminocarbonyl)-Ornithine N5-(Aminocarbonyl)ornithine N5-Carbamoyl-L-ornithine N5-carbamoylornithine N5-carbamylornithine Nγ-carbamylornithine N5-(Aminocarbonyl)-L-ornithine N5-(aminocarbonyl)ornithine ND-carbamylornithine Ndelta-carbamy-ornithine Ndelta-carbamylornithine Ngamma-carbamylornithine Sitrulline Ureidonorvaline Ureidovalerate Ureidovaleric acid α-amino-γ-Ureidovalerate α-amino-γ-Ureidovaleric acid α-amino-δ-Ureidovalerate α-amino-δ-Ureidovaleric acid δ-Ureidonorvaline C6H13N3O3 175.1857 175.095691297 (2S)-2-amino-5-(carbamoylamino)pentanoic acid L-citrulline 372-75-8 N[C@@H](CCCNC(N)=O)C(O)=O InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1 RHGKLRLOHDJJDR-BYPYZUCNSA-N Solid Cytosol logp -3.27 ALOGPS logs -0.90 ALOGPS solubility 2.18e+01 g/l ALOGPS melting_point 235.5 oC logp -3.9 ChemAxon pka_strongest_acidic 2.27 ChemAxon pka_strongest_basic 9.23 ChemAxon iupac (2S)-2-amino-5-(carbamoylamino)pentanoic acid ChemAxon average_mass 175.1857 ChemAxon mono_mass 175.095691297 ChemAxon smiles N[C@@H](CCCNC(N)=O)C(O)=O ChemAxon formula C6H13N3O3 ChemAxon inchi InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1 ChemAxon inchikey RHGKLRLOHDJJDR-BYPYZUCNSA-N ChemAxon polar_surface_area 118.44 ChemAxon refractivity 41.33 ChemAxon polarizability 17.35 ChemAxon rotatable_bond_count 5 ChemAxon acceptor_count 4 ChemAxon donor_count 4 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Alanine, aspartate and glutamate metabolism ec00250 Arginine and proline metabolism ec00330 Metabolic pathways eco01100 Aspartate metabolism Aspartate (seen in the center) is synthesized from and degraded to oxaloacetate , an intermediate of the TCA cycle, by a reversible transamination reaction with glutamate. As shown here, AspC is the principal transaminase that catalyzes this reaction, but TyrB also catalyzes it. Null mutations in aspC do not confer aspartate auxotrophy; null mutations in both aspC and tyrB do. Aspartate is a constituent of proteins and participates in several other biosyntheses as shown here( NAD biosynthesis and Beta-Alanine Metabolism . Approximately 27 percent of the cell's nitrogen flows through aspartate Aspartate can be synthesized from fumaric acid through a aspartate ammonia lyase. Aspartate also participates in the synthesis of L-asparagine through two different methods, either through aspartate ammonia ligase or asparagine synthetase B. Aspartate is also a precursor of fumaric acid. Again it has two possible ways of synthesizing it. First set of reactions follows an adenylo succinate synthetase that yields adenylsuccinic acid and then adenylosuccinate lyase in turns leads to fumaric acid. The second way is through argininosuccinate synthase that yields argininosuccinic acid and then argininosuccinate lyase in turns leads to fumaric acid PW000787 Metabolic 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 arginine biosynthesis I ARGSYN-PWY Specdb::CMs 671 Specdb::CMs 1793 Specdb::CMs 3348 Specdb::CMs 30500 Specdb::CMs 31260 Specdb::CMs 37834 Specdb::CMs 137170 Specdb::CMs 144904 Specdb::CMs 1081335 Specdb::CMs 1081337 Specdb::CMs 1081339 Specdb::CMs 1081341 Specdb::CMs 1081342 Specdb::CMs 1081344 Specdb::CMs 1081346 Specdb::NmrOneD 1281 Specdb::NmrOneD 1596 Specdb::NmrOneD 4747 Specdb::NmrOneD 20982 Specdb::NmrOneD 20983 Specdb::NmrOneD 20984 Specdb::NmrOneD 20985 Specdb::NmrOneD 20986 Specdb::NmrOneD 20987 Specdb::NmrOneD 20988 Specdb::NmrOneD 20989 Specdb::NmrOneD 20990 Specdb::NmrOneD 20991 Specdb::NmrOneD 20992 Specdb::NmrOneD 20993 Specdb::NmrOneD 20994 Specdb::NmrOneD 20995 Specdb::NmrOneD 20996 Specdb::NmrOneD 20997 Specdb::NmrOneD 20998 Specdb::NmrOneD 20999 Specdb::NmrOneD 21000 Specdb::NmrOneD 21001 Specdb::NmrOneD 166430 Specdb::MsMs 1286 Specdb::MsMs 1287 Specdb::MsMs 1288 Specdb::MsMs 4843 Specdb::MsMs 4844 Specdb::MsMs 4845 Specdb::MsMs 4846 Specdb::MsMs 4847 Specdb::MsMs 4848 Specdb::MsMs 4849 Specdb::MsMs 4850 Specdb::MsMs 4851 Specdb::MsMs 4852 Specdb::MsMs 4853 Specdb::MsMs 4854 Specdb::MsMs 4855 Specdb::MsMs 4856 Specdb::MsMs 4857 Specdb::MsMs 4858 Specdb::MsMs 4859 Specdb::MsMs 4860 Specdb::MsMs 4861 Specdb::MsMs 4862 Specdb::MsMs 4863 Specdb::MsMs 4864 Specdb::NmrTwoD 1044 Specdb::NmrTwoD 1537 HMDB00904 9750 9367 C00327 18211 L-CITRULLINE CIR Citrulline Keseler, I. 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Applied Microbiology (1971), 22(6), 992-9. http://hmdb.ca/system/metabolites/msds/000/000/816/original/HMDB00904.pdf?1358463111 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 Argininosuccinate synthase P0A6E4 ASSY_ECOLI argG http://ecmdb.ca/proteins/P0A6E4.xml Acetylornithine deacetylase P23908 ARGE_ECOLI argE http://ecmdb.ca/proteins/P23908.xml Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + Phosphate R01398 ORNCARBAMTRANSFER-RXN L-Aspartic acid + Adenosine triphosphate + Citrulline <> Adenosine monophosphate + Argininosuccinic acid + Hydrogen ion + Pyrophosphate R01954 Carbamoylphosphate + Ornithine <> Phosphate + Citrulline R01398 Adenosine triphosphate + Citrulline + L-Aspartic acid <> Adenosine monophosphate + Pyrophosphate + Argininosuccinic acid R01954 N-Acetyl-L-citrulline + Water <> Acetic acid + Citrulline R09107 L-Aspartic acid + Citrulline + Adenosine triphosphate > Hydrogen ion + L-arginino-succinate + Pyrophosphate + Adenosine monophosphate ARGSUCCINSYN-RXN Ornithine + Carbamoylphosphate <> Hydrogen ion + Citrulline + Phosphate R01398 ORNCARBAMTRANSFER-RXN Adenosine triphosphate + Citrulline + L-Aspartic acid > Adenosine monophosphate + Pyrophosphate + 2-(N(omega)-L-arginino)succinate Carbamoylphosphate + Ornithine > Inorganic phosphate + Citrulline Adenosine triphosphate + Citrulline + L-Aspartic acid + L-Aspartic acid > Pyrophosphate + Adenosine monophosphate + Argininosuccinic acid PW_R002649 Ornithine + Carbamoylphosphate + Ornithine > Phosphate + Hydrogen ion + Citrulline PW_R002676 L-Aspartic acid + Adenosine triphosphate + Citrulline <> Adenosine monophosphate + Argininosuccinic acid + Hydrogen ion + Pyrophosphate Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + Phosphate L-Aspartic acid + Adenosine triphosphate + Citrulline <> Adenosine monophosphate + Argininosuccinic acid + Hydrogen ion + Pyrophosphate 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 1350.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 5400000 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 931.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 3724000 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 516.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 2064000 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 38.4 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 153600 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 269.67 uM true 13.58 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 1078667 54308 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