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Metabolic Modeling Tutorial
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BioCyc websites down
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Metabolic Modeling Tutorial
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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) [Bonete96] , 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

Bonete96: 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 Dec 21, 2014, biocyc13.