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Identification
YMDB IDYMDB00592
NameL-Arginine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionArginine (abbreviated as Arg or R) is an alpha-amino acid. The L-isomer is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. It is classified as a polar, basic amino acid, because of the positively charged nature of the guanidino-alkyl side chain. With a pKa of 12.5, arginine is a positively amino acid at all physiological pHs. The first five steps of arginine biosynthesis in S. cerevisiae take place in the mitochondrion. This part of the pathway is known as the acetylated derivatives cycle because the acetyl group that is added to L-glutamate in the first step of the pathway is recycled via N-acetylglutamate generated in the fifth step. The enzymes that catalyze the second and third steps are encoded by a single gene (ARG5,6) that is translated into a pre-protein which is imported into mitochondria and cleaved there to yield two enzymes, N-acetylglutamate kinase and N-acetylglutamyl-phosphate reductase. These enzymes form a complex with each other and with N-acetylglutamate synthase, the first enzyme in the pathway, which may have implications for regulation of their activity. The mitochondrial steps of the arginine biosynthesis pathway result in the formation of ornithine, which is exported to the cytoplasm by the transporter Ort1p. In the cytoplasm, L-ornithine is converted to L-arginine in three reactions mediated by ornithine carbamoyltransferase, arginosuccinate synthase, and argininosuccinate lyase. The catabolism of arginine begins within the context of the urea cycle. It is hydrolyzed to urea and ornithine by arginase.
Structure
Thumb
Synonyms
  • (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
  • Arginine
  • L-(+)-Arginine
  • L-a-Amino-d-guanidinovalerate
  • L-a-Amino-d-guanidinovaleric acid
  • L-alpha-Amino-delta-guanidinovalerate
  • L-alpha-Amino-delta-guanidinovaleric acid
  • N5-(aminoiminomethyl)-L-Ornithine
  • (2S)-2-Amino-5-(carbamimidamido)pentanoic acid
  • (2S)-2-Amino-5-guanidinopentanoic acid
  • (S)-2-Amino-5-guanidinopentanoic acid
  • (S)-2-Amino-5-guanidinovaleric acid
  • Arg
  • L-Arg
  • L-Arginin
  • R
  • (2S)-2-Amino-5-(carbamimidamido)pentanoate
  • (2S)-2-Amino-5-guanidinopentanoate
  • (S)-2-Amino-5-guanidinopentanoate
  • (S)-2-Amino-5-guanidinovalerate
  • DL-Arginine acetate, monohydrate
  • L-Isomer arginine
  • Monohydrate DL-arginine acetate
  • L Arginine
  • Arginine, L isomer
  • Arginine, L-isomer
  • Hydrochloride, arginine
  • Arginine hydrochloride
  • DL Arginine acetate, monohydrate
CAS number74-79-3
WeightAverage: 174.201
Monoisotopic: 174.111675712
InChI KeyODKSFYDXXFIFQN-BYPYZUCNSA-N
InChIInChI=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
IUPAC Name(2S)-2-amino-5-carbamimidamidopentanoic acid
Traditional IUPAC NameL-arginine
Chemical FormulaC6H14N4O2
SMILESN[C@@H](CCCNC(N)=N)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Fatty acid
  • Guanidine
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carboximidamide
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point222 °C
Experimental Properties
PropertyValueReference
Water Solubility182 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-4.20 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility2.28 g/LALOGPS
logP-3.5ALOGPS
logP-3.2ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)2.41ChemAxon
pKa (Strongest Basic)12.41ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area125.22 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity53.92 m³·mol⁻¹ChemAxon
Polarizability17.8 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • mitochondrion
  • vacuole
  • cytoplasm
Organoleptic Properties
Flavour/OdourSource
FaintFDB002257
SMPDB Pathways
Glutamate MetabolismPW002376 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Arginine and proline metabolismec00330 Map00330
SMPDB Reactions
Argininosuccinic acid → Fumaric acid + L-Arginine
L-Arginine + waterOrnithine + Urea
KEGG Reactions
L-Arginine + waterOrnithine + Urea
Argininosuccinic acidL-Arginine + Fumaric acid
L-Arginine + Adenosine triphosphate + tRNA(Arg) → Adenosine monophosphate + Pyrophosphate + Arg-tRNA(Arg)
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
16662 ± 333 µM YPD mediaaerobicBaker's yeastPMID: 7654310
4180 ± 84 µM YPG mediaaerobicBaker's yeastPMID: 7654310
8773 ± 175 µM SD mediaaerobicBaker's yeastPMID: 7654310
3650 ± 73 µM SG mediaaerobicBaker's yeastPMID: 7654310
10951 ± 219 µM M (molasses)aerobicBaker's yeastPMID: 7654310
2355 ± 47 µM MA (molasses)aerobicBaker's yeastPMID: 7654310
5475 ± 109 µM MB (molasses)aerobicBaker's yeastPMID: 7654310
2708 ± 54 µM MAB (molasses)aerobicBaker's yeastPMID: 7654310
7005 ± 350 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
6020 ± 433 µM Synthetic medium with 20 g/L glucoseaerobicBaker's yeastPMID: 12584756
18000 ± 0 µM Minimal medium supplemented with ammonium and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
190000 ± 0 µM Minimal medium supplemented with arginine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
750 ± 750 µM Minimal medium supplemented with ornithine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
190000 ± 0 µM Minimal medium supplemented with citrulline and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
110000 ± 0 µM Minimal medium supplemented with citrulline and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • Martinez-Force, E., Benitez, T. (1995). "Effects of varying media, temperature, and growth rates on the intracellular concentrations of yeast amino acids." Biotechnol Prog 11:386-392.7654310
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Abadjieva, A., Pauwels, K., Hilven, P., Crabeel, M. (2001). "A new yeast metabolon involving at least the two first enzymes of arginine biosynthesis: acetylglutamate synthase activity requires complex formation with acetylglutamate kinase." J Biol Chem 276:42869-42880.11553611
  • Eisenstein, E., Osborne, J. C. Jr, Chaiken, I. M., Hensley, P. (1984). "Purification and characterization of ornithine transcarbamoylase from Saccharomyces cerevisiae." J Biol Chem 259:5139-5145.6370999
  • Hans, M. A., Heinzle, E., Wittmann, C. (2003). "Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae." Biotechnol Bioeng 82:143-151.12584756
  • Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). "The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism." BMC Syst Biol 2:71.18687109
  • Shimazu, M., Sekito, T., Akiyama, K., Ohsumi, Y., Kakinuma, Y. (2005). "A family of basic amino acid transporters of the vacuolar membrane from Saccharomyces cerevisiae." J Biol Chem 280:4851-4857.15572352
  • Gancedo, J. M., Gancedo, C. (1973). "Concentrations of intermediary metabolites in yeast." Biochimie 55:205-211.4578278
  • Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666
Synthesis Reference:Meyer, Helmut E.; Swiderek, Kristine; Hoffmann-Posorske, Edeltraut; Korte, Horst; Heilmeyer, Ludwig M. G., Jr. Quantitative determination of phosphoserine by high-performance liquid chromatography as the phenylthiocarbamyl-S-ethylcysteine. Application to
External Links:
ResourceLink
CHEBI ID16467
HMDB IDHMDB00517
Pubchem Compound ID6322
Kegg IDC00062
ChemSpider ID6082
FOODB IDFDB002257
WikipediaArginine
BioCyc IDARG

Enzymes

General function:
Involved in arginase activity
Specific function:
L-arginine + H(2)O = L-ornithine + urea
Gene Name:
CAR1
Uniprot ID:
P00812
Molecular weight:
35661.60156
Reactions
L-arginine + H(2)O → L-ornithine + urea.
General function:
Involved in argininosuccinate lyase activity
Specific function:
2-(N(omega)-L-arginino)succinate = fumarate + L-arginine
Gene Name:
ARG4
Uniprot ID:
P04076
Molecular weight:
51988.69922
Reactions
2-(N(omega)-L-arginino)succinate → fumarate + L-arginine.
General function:
Involved in nucleotide binding
Specific function:
ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)
Gene Name:
MSR1
Uniprot ID:
P38714
Molecular weight:
73693.39844
Reactions
ATP + L-arginine + tRNA(Arg) → AMP + diphosphate + L-arginyl-tRNA(Arg).
General function:
Involved in nucleotide binding
Specific function:
Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis
Gene Name:
Not Available
Uniprot ID:
Q05506
Molecular weight:
69524.39844
Reactions
ATP + L-arginine + tRNA(Arg) → AMP + diphosphate + L-arginyl-tRNA(Arg).

Transporters

General function:
Involved in transport
Specific function:
Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
Gene Name:
GAP1
Uniprot ID:
P19145
Molecular weight:
65654.89844
General function:
Involved in transmembrane transport
Specific function:
Transporter required for vacuolar uptake of histidine, arginine and lysine and to a lesser extent tyrosine
Gene Name:
VBA2
Uniprot ID:
P38358
Molecular weight:
51676.39844
General function:
Involved in transport
Specific function:
High-affinity permease for basic amino acids
Gene Name:
ALP1
Uniprot ID:
P38971
Molecular weight:
64012.89844
General function:
Involved in transport
Specific function:
High-affinity permease for arginine
Gene Name:
CAN1
Uniprot ID:
P04817
Molecular weight:
65784.79688