2.0 2012-05-31 10:27:12 -0600 2015-09-13 12:56:08 -0600 ECMDB00517 M2MDB000146 L-Arginine Arginine is an amino acid that is physiologically active in the L-form. Arginine can be considered to be a basic amino acid as the part of the side chain nearest to the backbone is long, carbon-containing and hydrophobic, whereas the end of the side chain is a complex guanidinium group. With a pKa of 12.48, the guanidinium group is positively charged in neutral, acidic and even most basic environments. Because of the conjugation between the double bond and the nitrogen lone pairs, the positive charge is delocalized. This group is able to form multiple H-bonds. The main catabolic arginine pathway of Escherichia coli K-12 is the succinyltransferase pathway. (PMID: 9696779) (S)-2-amino-5-[(aminoiminomethyl)amino]-Pentanoate (S)-2-amino-5-[(aminoiminomethyl)amino]-Pentanoic acid (S)-2-Amino-5-[(aminoiminomethyl)amino]pentanoate (S)-2-Amino-5-[(aminoiminomethyl)amino]pentanoic acid 2-Amino-5-guanidinovalerate 2-Amino-5-guanidinovaleric acid 5-[(Aminoiminomethyl)amino]-L-Norvaline Arg Arginine L-(+)-Arginine L-a-Amino-D-guanidinovalerate L-a-Amino-D-guanidinovaleric acid L-a-Amino-delta-guanidinovalerate L-a-Amino-delta-guanidinovaleric acid L-a-amino-δ-Guanidinovalerate L-a-amino-δ-Guanidinovaleric acid L-alpha-Amino-delta-guanidinovalerate L-alpha-Amino-delta-guanidinovaleric acid L-α-amino-δ-Guanidinovalerate L-α-amino-δ-Guanidinovaleric acid N5-(aminoiminomethyl)-L-Ornithine R C6H14N4O2 174.201 174.111675712 (2S)-2-amino-5-carbamimidamidopentanoic acid L-arginine 74-79-3 N[C@@H](CCCNC(N)=N)C(O)=O InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m0/s1 ODKSFYDXXFIFQN-BYPYZUCNSA-N Solid Cytosol Extra-organism Periplasm logp -3.49 ALOGPS logs -1.88 ALOGPS solubility 2.28e+00 g/l ALOGPS melting_point 222 oC logp -3.2 ChemAxon pka_strongest_acidic 2.41 ChemAxon pka_strongest_basic 12.41 ChemAxon iupac (2S)-2-amino-5-carbamimidamidopentanoic acid ChemAxon average_mass 174.201 ChemAxon mono_mass 174.111675712 ChemAxon smiles N[C@@H](CCCNC(N)=N)C(O)=O ChemAxon formula C6H14N4O2 ChemAxon inchi InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m0/s1 ChemAxon inchikey ODKSFYDXXFIFQN-BYPYZUCNSA-N ChemAxon polar_surface_area 125.22 ChemAxon refractivity 53.92 ChemAxon polarizability 17.8 ChemAxon rotatable_bond_count 5 ChemAxon acceptor_count 6 ChemAxon donor_count 5 ChemAxon physiological_charge 1 ChemAxon formal_charge 0 ChemAxon Alanine, aspartate and glutamate metabolism ec00250 Arginine and proline metabolism ec00330 Aminoacyl-tRNA biosynthesis ec00970 ABC transporters ec02010 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 tRNA Charging 2 This pathway groups together all E. coli tRNA charging reactions. PW000803 Metabolic tRNA charging This pathway groups together all E. coli tRNA charging reactions. PW000799 Metabolic tRNA charging TRNA-CHARGING-PWY arginine biosynthesis I ARGSYN-PWY arginine degradation II (AST pathway) AST-PWY arginine degradation III (arginine decarboxylase/agmatinase pathway) PWY0-823 putrescine biosynthesis I PWY-40 arginine dependent acid resistance PWY0-1299 Specdb::CMs 569 Specdb::CMs 570 Specdb::CMs 1414 Specdb::CMs 1500 Specdb::CMs 2989 Specdb::CMs 30365 Specdb::CMs 30765 Specdb::CMs 31160 Specdb::CMs 31161 Specdb::CMs 32272 Specdb::CMs 37588 Specdb::CMs 132665 Specdb::CMs 140399 Specdb::CMs 1064714 Specdb::CMs 1064716 Specdb::CMs 1064718 Specdb::CMs 1064719 Specdb::CMs 1064721 Specdb::CMs 1064723 Specdb::CMs 1064724 Specdb::CMs 1064726 Specdb::CMs 1064728 Specdb::NmrOneD 1236 Specdb::NmrOneD 1404 Specdb::NmrOneD 4923 Specdb::NmrOneD 144190 Specdb::NmrOneD 144191 Specdb::NmrOneD 144192 Specdb::NmrOneD 144193 Specdb::NmrOneD 144194 Specdb::NmrOneD 144195 Specdb::NmrOneD 144196 Specdb::NmrOneD 144197 Specdb::NmrOneD 144198 Specdb::NmrOneD 144199 Specdb::NmrOneD 144200 Specdb::NmrOneD 144201 Specdb::NmrOneD 144202 Specdb::NmrOneD 144203 Specdb::NmrOneD 144204 Specdb::NmrOneD 144205 Specdb::NmrOneD 144206 Specdb::NmrOneD 144207 Specdb::NmrOneD 144208 Specdb::NmrOneD 144209 Specdb::NmrOneD 166444 Specdb::MsMs 740 Specdb::MsMs 741 Specdb::MsMs 742 Specdb::MsMs 4157 Specdb::MsMs 4158 Specdb::MsMs 4159 Specdb::MsMs 4160 Specdb::MsMs 4161 Specdb::MsMs 4162 Specdb::MsMs 4163 Specdb::MsMs 4164 Specdb::MsMs 4165 Specdb::MsMs 4166 Specdb::MsMs 4167 Specdb::MsMs 4168 Specdb::MsMs 4169 Specdb::MsMs 4170 Specdb::MsMs 4171 Specdb::MsMs 4172 Specdb::MsMs 4175 Specdb::MsMs 4176 Specdb::MsMs 4177 Specdb::MsMs 4178 Specdb::MsMs 4179 Specdb::MsMs 4180 Specdb::NmrTwoD 1022 Specdb::NmrTwoD 1348 HMDB00517 6322 6082 C00062 16467 ARG GND L-Arginine Keseler, I. 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Application to http://hmdb.ca/system/metabolites/msds/000/000/436/original/HMDB00517.pdf?1358894658 Histidine transport ATP-binding protein hisP P07109 HISP_ECOLI hisP http://ecmdb.ca/proteins/P07109.xml Arginine N-succinyltransferase P0AE37 ASTA_ECOLI astA http://ecmdb.ca/proteins/P0AE37.xml Argininosuccinate lyase P11447 ARLY_ECOLI argH http://ecmdb.ca/proteins/P11447.xml Arginyl-tRNA synthetase P11875 SYR_ECOLI argS http://ecmdb.ca/proteins/P11875.xml Biosynthetic arginine decarboxylase P21170 SPEA_ECOLI speA http://ecmdb.ca/proteins/P21170.xml Biodegradative arginine decarboxylase P28629 ADIA_ECOLI adiA http://ecmdb.ca/proteins/P28629.xml Putative ABC transporter arginine-binding protein 2 P30859 ARTI_ECOLI artI http://ecmdb.ca/proteins/P30859.xml ABC transporter arginine-binding protein 1 P30860 ARTJ_ECOLI artJ http://ecmdb.ca/proteins/P30860.xml Arginine ABC transporter permease protein ArtQ P0AE34 ARTQ_ECOLI artQ http://ecmdb.ca/proteins/P0AE34.xml Arginine ABC transporter permease protein ArtM P0AE30 ARTM_ECOLI artM http://ecmdb.ca/proteins/P0AE30.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 Arginine transport ATP-binding protein ArtP P0AAF6 ARTP_ECOLI artP http://ecmdb.ca/proteins/P0AAF6.xml Histidine transport ATP-binding protein hisP P07109 HISP_ECOLI hisP http://ecmdb.ca/proteins/P07109.xml Putative ABC transporter arginine-binding protein 2 P30859 ARTI_ECOLI artI http://ecmdb.ca/proteins/P30859.xml ABC transporter arginine-binding protein 1 P30860 ARTJ_ECOLI artJ http://ecmdb.ca/proteins/P30860.xml Arginine ABC transporter permease protein ArtM P0AE32 ARTM_ECO57 artM http://ecmdb.ca/proteins/P0AE32.xml Arginine ABC transporter permease protein ArtQ P0AE34 ARTQ_ECOLI artQ http://ecmdb.ca/proteins/P0AE34.xml Uncharacterized amino-acid ABC transporter ATP-binding protein yecC P37774 YECC_ECOLI yecC http://ecmdb.ca/proteins/P37774.xml Inner membrane amino-acid ABC transporter permease protein yecS P0AFT2 YECS_ECOLI yecS http://ecmdb.ca/proteins/P0AFT2.xml Arginine ABC transporter permease protein ArtM P0AE30 ARTM_ECOLI artM http://ecmdb.ca/proteins/P0AE30.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 Arginine transport ATP-binding protein ArtP P0AAF6 ARTP_ECOLI artP http://ecmdb.ca/proteins/P0AAF6.xml Arginine/agmatine antiporter P60061 ADIC_ECOLI adiC http://ecmdb.ca/proteins/P60061.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Arginine exporter protein ArgO P11667 ARGO_ECOLI argO http://ecmdb.ca/proteins/P11667.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml Adenosine triphosphate + Water + L-Arginine > ADP + L-Arginine + Hydrogen ion + Phosphate ABC-4-RXN Adenosine triphosphate + Water + L-Arginine > ADP + L-Arginine + Hydrogen ion + Phosphate ABC-4-RXN L-Arginine + Succinyl-CoA <> Coenzyme A + Hydrogen ion + N2-Succinyl-L-arginine R00832 ARGININE-N-SUCCINYLTRANSFERASE-RXN L-Arginine + Adenosine triphosphate + tRNA(Arg) + tRNA(Arg) <> Adenosine monophosphate + L-Arginyl-tRNA(Arg) + Pyrophosphate + L-Arginyl-tRNA(Arg) R03646 L-Arginine + Hydrogen ion <> Agmatine + Carbon dioxide R00566 ARGDECARBOX-RXN Argininosuccinic acid <> L-Arginine + Fumaric acid R01086 L-Arginine + Hydrogen ion > Agmatine + Carbon dioxide L-Arginine <> Agmatine + Carbon dioxide R00566 Succinyl-CoA + L-Arginine <> Coenzyme A + N2-Succinyl-L-arginine R00832 Adenosine triphosphate + L-Arginine + tRNA(Arg) <> Adenosine monophosphate + Pyrophosphate + L-Arginyl-tRNA(Arg) R03646 Adenosine triphosphate + L-Arginine + Water > ADP + Phosphate + L-Arginine + Hydrogen ion ABC-4-RXN Adenosine triphosphate + L-Arginine + Water > ADP + Phosphate + L-Arginine + Hydrogen ion ABC-4-RXN L-Arginine + Succinyl-CoA > Hydrogen ion + N2-Succinyl-L-arginine + Coenzyme A ARGININE-N-SUCCINYLTRANSFERASE-RXN L-arginino-succinate <> L-Arginine + Fumaric acid ARGSUCCINLYA-RXN General-Protein-Substrates L-Arginine + Peptides RXN0-3261 L-Arginine > Agmatine + Carbon dioxide 2-(N(omega)-L-arginino)succinate > Fumaric acid + L-Arginine Succinyl-CoA + L-Arginine > CoA + N2-Succinyl-L-arginine Adenosine triphosphate + L-Arginine + tRNA(Arg) > Adenosine monophosphate + Pyrophosphate + L-arginyl-tRNA(Arg) Argininosuccinic acid > Fumaric acid + L-Arginine PW_R002652 L-Arginine + Succinyl-CoA + Succinyl-CoA > Coenzyme A + Hydrogen ion + N2-succinyl-L-arginine + N2-succinyl-L-arginine PW_R002678 L-Arginine + Hydrogen ion + Carbon dioxide > Agmatine PW_R002683 L-Arginine + tRNA(Arg) + Adenosine triphosphate + Hydrogen ion > Pyrophosphate + Adenosine monophosphate + L-arginyl-tRNA(Arg) PW_R002823 L-Arginine + Adenosine triphosphate + Water > L-Arginine + Adenosine diphosphate + Phosphate + Hydrogen ion + ADP PW_RCT000101 L-Arginine + Adenosine triphosphate + Water > L-Arginine + Adenosine diphosphate + Phosphate + Hydrogen ion + ADP PW_RCT000101 L-Arginine + Succinyl-CoA <> Coenzyme A + Hydrogen ion + N2-Succinyl-L-arginine L-Arginine + Hydrogen ion <> Agmatine + Carbon dioxide L-Arginine + Adenosine triphosphate + tRNA(Arg) <> Adenosine monophosphate + L-Arginyl-tRNA(Arg) + Pyrophosphate Argininosuccinic acid <> L-Arginine + Fumaric acid L-Arginine + Hydrogen ion <> Agmatine + Carbon dioxide L-Arginine + Succinyl-CoA <> Coenzyme A + Hydrogen ion + N2-Succinyl-L-arginine L-Arginine + Adenosine triphosphate + tRNA(Arg) <> Adenosine monophosphate + L-Arginyl-tRNA(Arg) + 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 569.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 2276000 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 57.5 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 230000 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 389.67 uM true 23.8 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 1558667 95191 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