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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: L-arginine

Abbrev Name: arg

Synonyms: 2-amino-5-guanidinovaleric acid, R, arginine, arg, L-arg

Superclasses: an amino acid or its derivative an amino acid a basic amino acid
an amino acid or its derivative an amino acid a polar amino acid a positively-charged polar amino acid
an amino acid or its derivative an amino acid an alpha amino acid a standard alpha amino acid
an amino acid or its derivative an amino acid an L-amino acid

Chemical Formula: C6H15N4O2

Molecular Weight: 175.21 Daltons

Monoisotopic Molecular Weight: 174.1116757144 Daltons

pKa 1: 2.18

SMILES: C(NC(N)=[N+])CCC([N+])C(=O)[O-]

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)/p+1/t4-/m0/s1

InChIKey: InChIKey=ODKSFYDXXFIFQN-BYPYZUCNSA-O

Unification Links: CAS:74-79-3 , ChEBI:32682 , ChemSpider:1266045 , HMDB:HMDB00517 , IAF1260:33707 , KEGG:C00062 , MetaboLights:MTBLC32682 , PubChem:1549073

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): 79.88474 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

arginine degradation II (AST pathway) :
L-arginine + succinyl-CoA → N2-succinyl-L-arginine + coenzyme A + H+

arginine degradation VIII (arginine oxidase pathway) :
L-arginine + oxygen + H2O → ammonium + 2-ketoarginine + hydrogen peroxide

arginine degradation X (arginine monooxygenase pathway) :
L-arginine + oxygen → 4-guanidinobutyramide + CO2 + H2O

citrulline-nitric oxide cycle , nitric oxide biosynthesis (plants) :
2 L-arginine + 3 NADPH + H+ + 4 oxygen → 2 L-citrulline + 2 nitric oxide + 3 NADP+ + 4 H2O

clavulanate biosynthesis :
D-glyceraldehyde 3-phosphate + L-arginine → L-N2-(2-carboxyethyl)arginine + phosphate + H+

creatine biosynthesis :
glycine + L-arginine → guanidinoacetate + L-ornithine

cyanophycin metabolism :
cyanophycin primer-L-aspartate + L-arginine + ATP → cyanophycin + ADP + phosphate
[cyanophycin]-L-aspartate + L-arginine + ATP → cyanophycin + ADP + phosphate

D-cycloserine biosynthesis :
L-arginine + 2-oxoglutarate + oxygen → Nω-hydroxy-L-arginine + succinate + CO2

ethylene biosynthesis II (microbes) :
L-arginine + 2-oxoglutarate + oxygen → (3S)-3-hydroxy-L-arginine + succinate + CO2

ethylene biosynthesis IV :
2-oxoglutarate + L-arginine + oxygen → succinate + CO2 + guanidinium + (S)-1-pyrroline-5-carboxylate + H2O + H+

pyoverdine I biosynthesis :
L-glutamate + L-tyrosine + L-2,4-diaminobutanoate + 2 L-serine + L-arginine + 2 N5-formyl-N5-hydroxy-L-ornithine + L-lysine + 2 L-threonine → ferribactin + 2 H+ + 12 H2O

pyruvate fermentation to opines :
D-octopine + NAD+ + H2O ← L-arginine + pyruvate + NADH + H+

rhizocticin A and B biosynthesis :
ATP + 2-amino-4-hydroxy-5-phosphonopentanoate + L-arginine → ADP + L-arginyl-4-hydroxy-5-phosphonopentanoate + phosphate + H+
ATP + L-2-amino-5-phosphono-3-cis-pentenoate + L-arginine → ADP + rhizocticin A + phosphate + H+

streptomycin biosynthesis :
N1-amidinostreptamine 6-phosphate + L-arginine → streptidine 6-phosphate + L-ornithine
L-arginine + 1-amino-1-deoxy-scyllo-inositol 4-phosphate → 1-guanidino-1-deoxy-scyllo-inositol 4-phosphate + L-ornithine

tRNA charging :
tRNAarg + L-arginine + ATP + H+ → L-arginyl-tRNAarg + AMP + diphosphate

Not in pathways:
D-nopaline + NADP+ + H2O ← L-arginine + 2-oxoglutarate + NADPH + H+
3 2-oxoglutarate + L-arginine + 3 oxygen + 3 H+ → 2 ethylene + 7 CO2 + succinate + guanidinium + (S)-1-pyrroline-5-carboxylate + 3 H2O
2 L-arginine + 3 NAD(P)H + H+ + 4 oxygen → 2 L-citrulline + 2 nitric oxide + 3 NAD(P)+ + 4 H2O
L-tyrosine + L-arginine + ATP → L-tyrosyl-L-arginine + AMP + diphosphate + H+

γ-glutamyl cycle :
glutathione + a standard α amino acid → L-cysteinyl-glycine + an (γ-L-glutamyl)-L-amino acid

leukotriene biosynthesis :
leukotriene-C4 + a standard α amino acid → an (γ-L-glutamyl)-L-amino acid + leukotriene-D4

methanofuran biosynthesis :
2-furaldehyde phosphate + a standard α amino acid → 2-methylamine-furan phosphate + a 2-oxo carboxylate


a standard α amino acid + oxygen + H2O → ammonium + hydrogen peroxide + a 2-oxo carboxylate

prodigiosin biosynthesis :
(S)-3-acetyloctanal + an L-amino acid → 2-methyl-3-n-amyl-dihydropyrrole + a 2-oxo acid + H2O

rhizocticin A and B biosynthesis :
2-keto-5-phosphono-3-cis-pentenoate + an L-amino acidL-2-amino-5-phosphono-3-cis-pentenoate + a 2-oxo carboxylate
2-keto-4-hydroxy-5-phosphonopentanoate + an L-amino acid → 2-amino-4-hydroxy-5-phosphonopentanoate + a 2-oxo carboxylate


ATP + 2 an L-amino acid → ADP + a dipeptide + phosphate + H+

Reactions known to produce the compound:

D-arginine degradation :
2-ketoarginine + ammonium + NAD(P)H → L-arginine + NAD(P)+

nopaline degradation :
D-nopaline + an oxidized electron acceptor + H2O → 2-oxoglutarate + L-arginine + a reduced electron acceptor

octopine degradation :
D-octopine + an oxidized electron acceptor + H2O → pyruvate + L-arginine + a reduced electron acceptor

Not in pathways:
Nω-(ADP-D-ribosyl)-L-arginine + H2O → ADP-D-ribose + L-arginine
a protein[periplasmic space] + H2O[periplasmic space] → a peptide[periplasmic space] + L-arginine[periplasmic space]

dimethylsulfoniopropionate biosynthesis I (Wollastonia) :
S-methyl-L-methionine + a 2-oxo carboxylate + H+ → 3-dimethylsulfoniopropionaldehyde + CO2 + a standard α amino acid

seed germination protein turnover , wound-induced proteolysis I :
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)


a dipeptide + H2O → 2 amino acids
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
β-aspartyl dipeptide + H2O → L-aspartate + a standard α amino acid
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a dipeptide + H2O → 2 a standard α amino acid
a peptide + H2O → a standard α amino acid + a peptide
a peptide + H2O → a peptide + a standard α amino acid
a peptide + H2O → a peptide + a standard α amino acid
an oligopeptide + H2O → a peptide + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a protein + H2O → a standard α amino acid + a peptide
a peptide + H2O → a standard α amino acid + a peptide
a protein + H2O → a standard α amino acid + a peptide
a tripeptide + H2O → a dipeptide + a standard α amino acid
a dipetide with L-aspartate at the N-terminal + H2O → L-aspartate + a standard α amino acid
a dipetide with L-histidine at the C-terminal + H2O → a standard α amino acid + L-histidine
a dipeptide with L-methionine at the N-terminal + H2O → a standard α amino acid + L-methionine
a dipeptide with proline at the C-terminal + H2O → L-proline + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)


a protein with a basic C-terminal amino-acid + H2O → a peptide + a basic amino acid
a protein + H2O → a basic amino acid + a protein
a peptide + H2O → a basic amino acid + a peptide
a peptide + H2O → a basic amino acid + a peptide
a peptide + H2O → a peptide + a basic amino acid
a peptide + H2O → a basic amino acid + a peptide

γ-glutamyl cycle :
an (γ-L-glutamyl)-L-amino acid → an L-amino acid + 5-oxoproline


a peptide + H2O → an L-amino acid + a peptide
a peptide + H2O → a peptide + an L-amino acid
a N-methyl L-amino acid + oxygen + H2O → an L-amino acid + formaldehyde + hydrogen peroxide
a polypeptide + H2O → a polypeptide + an L-amino acid


amino acids(n) + H2O → amino acids(n-1) + an α amino acid
an α amino acid ester + H2O → an alcohol + an α amino acid + H+
a protein + H2O → a protein + an α amino acid

Reactions known to both consume and produce the compound:

arginine biosynthesis I (via L-ornithine) , arginine biosynthesis II (acetyl cycle) , arginine biosynthesis III (via N-acetyl-L-citrulline) , arginine biosynthesis IV (archaebacteria) , citrulline-nitric oxide cycle :
L-arginino-succinate ↔ L-arginine + fumarate

arginine degradation I (arginase pathway) , arginine degradation VI (arginase 2 pathway) , arginine degradation VII (arginase 3 pathway) , citrulline biosynthesis , L-Nδ-acetylornithine biosynthesis :
L-arginine + H2O ↔ urea + L-ornithine

arginine degradation III (arginine decarboxylase/agmatinase pathway) , arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) , arginine dependent acid resistance , putrescine biosynthesis I , putrescine biosynthesis II , spermidine biosynthesis III :
L-arginine + H+ ↔ CO2 + agmatine

arginine degradation IX (arginine:pyruvate transaminase pathway) :
L-arginine + pyruvate ↔ 2-ketoarginine + L-alanine

arginine degradation V (arginine deiminase pathway) , proline biosynthesis II (from arginine) :
L-arginine + H2O ↔ ammonium + L-citrulline

arginine degradation XI :
L-arginine + 2-oxoglutarate ↔ L-glutamate + 2-ketoarginine

arginine degradation XII :
L-arginine + a deaminated amino group acceptor ↔ 2-ketoarginine + an aminated amino group acceptor

putrescine biosynthesis IV :
L-arginine + H2O ↔ urea + L-ornithine
L-arginine + H+ ↔ CO2 + agmatine

urea cycle :
L-arginino-succinate ↔ L-arginine + fumarate
L-arginine + H2O ↔ urea + L-ornithine

Not in pathways:
L-arginine ↔ D-arginine
L-arginine + ATP ↔ Nω-phospho-L-arginine + ADP + H+

asparagine degradation II :
a 2-oxo carboxylate + L-asparagine ↔ 2-oxosuccinamate + a standard α amino acid

dimethylsulfoniopropionate biosynthesis III (algae) , ethylene biosynthesis III (microbes) :
L-methionine + a 2-oxo carboxylate ↔ 2-oxo-4-methylthiobutanoate + a standard α amino acid

glucosinolate biosynthesis from dihomomethionine :
2-oxo-6-methylthiohexanoate + a standard α amino acid ↔ L-dihomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from hexahomomethionine :
2-oxo-10-methylthiodecanoate + a standard α amino acid ↔ hexahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from pentahomomethionine :
2-oxo-9-methylthiononanoate + a standard α amino acid ↔ pentahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from tetrahomomethionine :
2-oxo-8-methylthiooctanoate + a standard α amino acid ↔ tetrahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from trihomomethionine :
2-oxo-7-methylthioheptanoate + a standard α amino acid ↔ trihomomethionine + a 2-oxo carboxylate

homomethionine biosynthesis :
2-oxo-5-methylthiopentanoate + a standard α amino acid ↔ L-homomethionine + a 2-oxo carboxylate
L-methionine + a 2-oxo carboxylate ↔ 2-oxo-4-methylthiobutanoate + a standard α amino acid


L-ornithine + a 2-oxo carboxylate ↔ a standard α amino acid + L-glutamate-5-semialdehyde


L-alanine + a 2-oxo carboxylate ↔ pyruvate + an L-amino acid

In Reactions of unknown directionality:

Not in pathways:
2 L-arginine + 2 NADPH + 2 H+ + 2 oxygen = 2 Nω-hydroxy-L-arginine + 2 NADP+ + 2 H2O
2 L-arginine + 2 NAD(P)H + 2 H+ + 2 oxygen = 2 Nω-hydroxy-L-arginine + 2 NAD(P)+ + 2 H2O
L-arginine + L-lysine = homoarginine + L-ornithine


an L-amino acid = a D-amino acid
an L-amino acid + NAD+ + H2O = a 2-oxo carboxylate + ammonium + NADH + H+
an N-carbamoyl-L-amino acid + H2O + 2 H+ = an L-amino acid + ammonium + CO2
S-ureidoglycine + a 2-oxo carboxylate = oxalurate + an L-amino acid


a 5-L-glutamyl-[peptide] + an amino acid = a 5-L-glutamyl-amino acid + a peptide

In Transport reactions:
L-glutamine[out] + L-arginine[in] → L-glutamine[in] + L-arginine[out] ,
L-arginine[out]L-arginine[in] ,
agmatine[cytosol] + L-arginine[periplasmic space] → agmatine[periplasmic space] + L-arginine[cytosol] ,
ATP + L-arginine[periplasmic space] + H2O → ADP + L-arginine[cytosol] + phosphate + H+ ,
a polar amino acid[extracellular space] + ATP + H2O ↔ a polar amino acid[cytosol] + ADP + phosphate ,
an L-amino acid[cytosol]an L-amino acid[periplasmic space]

Enzymes activated by L-arginine, sorted by the type of activation, are:

Activator (Allosteric) of: ornithine succinyltransferase [Tricot94]

Activator (Mechanism unknown) of: ornithine carbamoyltransferase, catabolic [Ruepp95] , glutamate dehydrogenase (NAD-dependent) [Bonete96a] , ornithine cyclodeaminase [Sans88] , arginase

Enzymes inhibited by L-arginine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: agmatinase [Satishchandran86] , lysine:cadaverine antiporter [Soksawatmaekhin04]

Inhibitor (Mechanism unknown) of: N-acetylglutamate synthase [Marvil77] , D-octopine synthase [Schrimsher84] , S-methyl-L-methionine decarboxylase [Kocsis00] , acetylglutamate kinase , carbamoyl-phosphate synthetase, arginine specific [Paulus79] , homocitrate synthase [Wulandari02]


References

Bonete96a: Bonete MJ, Perez-Pomares F, Ferrer J, Camacho ML (1996). "NAD-glutamate dehydrogenase from Halobacterium halobium: inhibition and activation by TCA intermediates and amino acids." Biochim Biophys Acta 1996;1289(1);14-24. PMID: 8605224

Kocsis00: Kocsis MG, Hanson AD (2000). "Biochemical evidence for two novel enzymes in the biosynthesis of 3-dimethylsulfoniopropionate in Spartina alterniflora." Plant Physiol 123(3);1153-61. PMID: 10889264

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Marvil77: Marvil DK, Leisinger T (1977). "N-acetylglutamate synthase of Escherichia coli: purification, characterization, and molecular properties." J Biol Chem 1977;252(10);3295-303. PMID: 16890

Paulus79: Paulus TJ, Switzer RL (1979). "Characterization of pyrimidine-repressible and arginine-repressible carbamyl phosphate synthetases from Bacillus subtilis." J Bacteriol 1979;137(1);82-91. PMID: 216664

Ruepp95: Ruepp A, Muller HN, Lottspeich F, Soppa J (1995). "Catabolic ornithine transcarbamylase of Halobacterium halobium (salinarium): purification, characterization, sequence determination, and evolution." J Bacteriol 1995;177(5);1129-36. PMID: 7868583

Sans88: Sans N, Schindler U, Schroder J (1988). "Ornithine cyclodeaminase from Ti plasmid C58: DNA sequence, enzyme properties and regulation of activity by arginine." Eur J Biochem 173(1);123-30. PMID: 3281832

Satishchandran86: Satishchandran C, Boyle SM (1986). "Purification and properties of agmatine ureohydrolyase, a putrescine biosynthetic enzyme in Escherichia coli." J Bacteriol 1986;165(3);843-8. PMID: 3081491

Schrimsher84: Schrimsher JL, Taylor KB (1984). "Octopine dehydrogenase from Pecten maximus: steady-state mechanism." Biochemistry 23(7);1348-53. PMID: 6722094

Soksawatmaekhin04: Soksawatmaekhin W, Kuraishi A, Sakata K, Kashiwagi K, Igarashi K (2004). "Excretion and uptake of cadaverine by CadB and its physiological functions in Escherichia coli." Mol Microbiol 51(5);1401-12. PMID: 14982633

Tricot94: Tricot C, Vander Wauven C, Wattiez R, Falmagne P, Stalon V (1994). "Purification and properties of a succinyltransferase from Pseudomonas aeruginosa specific for both arginine and ornithine." Eur J Biochem 224(3);853-61. PMID: 7523119

Wulandari02: Wulandari AP, Miyazaki J, Kobashi N, Nishiyama M, Hoshino T, Yamane H (2002). "Characterization of bacterial homocitrate synthase involved in lysine biosynthesis." FEBS Lett 522(1-3);35-40. PMID: 12095615


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, BIOCYC13B.