You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Ornithine (YMDB00353)

Identification
YMDB IDYMDB00353
NameOrnithine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionOrnithine, also known as (S)-ornithine, 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. Ornithine is a very strong basic compound (based on its pKa). Ornithine exists in all living species, ranging from bacteria to humans. Ornithine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (+)-S-Ornithine
  • (S)-2,5-Diaminopentanoate
  • (S)-2,5-Diaminopentanoic acid
  • (S)-a,d-Diaminovalerate
  • (S)-a,d-Diaminovaleric acid
  • (S)-Ornithine
  • 5-amino-L-Norvaline
  • L-(-)-Ornithine
  • L-Ornithine
  • (S)-2,5-Diaminovaleric acid
  • (S)-alpha,delta-Diaminovaleric acid
  • (S)-2,5-Diaminovalerate
  • (S)-a,delta-Diaminovalerate
  • (S)-a,delta-Diaminovaleric acid
  • (S)-alpha,delta-Diaminovalerate
  • (S)-Α,δ-diaminovalerate
  • (S)-Α,δ-diaminovaleric acid
  • (S)-a,Δ-diaminovalerate
  • (S)-a,Δ-diaminovaleric acid
  • 2,5-Diaminopentanoic acid
  • Ornithine dihydrochloride, (L)-isomer
  • Ornithine hydrochloride, (D)-isomer
  • Ornithine, (D)-isomer
  • Ornithine, (L)-isomer
  • 2,5 Diaminopentanoic acid
  • Ornithine monoacetate, (L)-isomer
  • Ornithine monohydrochloride, (D)-isomer
  • Ornithine monohydrochloride, (DL)-isomer
  • Ornithine phosphate (1:1), (L)-isomer
  • Ornithine sulfate (1:1), (L)-isomer
  • Ornithine hydrochloride, (DL)-isomer
  • Ornithine hydrochloride, (L)-isomer
  • Ornithine monohydrobromide, (L)-isomer
  • Ornithine, (DL)-isomer
CAS number70-26-8
WeightAverage: 132.161
Monoisotopic: 132.089877638
InChI KeyAHLPHDHHMVZTML-BYPYZUCNSA-N
InChIInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
IUPAC Name(2S)-2,5-diaminopentanoic acid
Traditional IUPAC Nameornithine
Chemical FormulaC5H12N2O2
SMILES[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]
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
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point140 °C
Experimental Properties
PropertyValueReference
Water Solubility620 mg/mL [HMP experimental]PhysProp
LogP-4.22 [SANGSTER (1994)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility172 g/LALOGPS
logP-3.6ALOGPS
logP-3.7ChemAxon
logS0.11ALOGPS
pKa (Strongest Acidic)2.67ChemAxon
pKa (Strongest Basic)10.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity33.21 m³·mol⁻¹ChemAxon
Polarizability13.85 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm, Extracellular, Mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Glutamate MetabolismPW002376 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW002381 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
beta-Alanine metabolismec00410 Map00410
SMPDB Reactions
L-Arginine + water → Ornithine + Urea
Ornithine + Oxoglutaric acid ↔ L-Glutamic acid + l-Glutamic-gamma-semialdehyde
Ornithine + hydron → Carbon dioxide + Putrescine
KEGG Reactions
L-Arginine + water → Ornithine + Urea
Ornithine + Carbamoylphosphate → Citrulline + phosphate + hydron
Ornithine + hydron → Putrescine + Carbon dioxide
L-Glutamic acid + N-Acetylornithine → N-acetyl-L-glutamic acid + Ornithine
Oxoglutaric acid + Ornithine → L-Glutamic acid + l-Glutamic-gamma-semialdehyde
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
132 ± 7 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
7000 ± 0 µM Minimal medium supplemented with ammonium and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
20000 ± 0 µM Minimal medium supplemented with arginine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
330000 ± 0 µM Minimal medium supplemented with ornithine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
22000 ± 0 µM Minimal medium supplemented with citrulline and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • 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
  • Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway." FEBS J 275:4111-4120.18625006
  • Gancedo, J. M., Gancedo, C. (1973). "Concentrations of intermediary metabolites in yeast." Biochimie 55:205-211.4578278
Synthesis Reference:Zhang, Peng; Zhang, Shurong; Liu, Chunqiao; Yang, Yuhong. Method for preparing L-ornithine by enzymatic conversion. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 8pp.
External Links:
ResourceLink
CHEBI ID15729
HMDB IDHMDB00214
Pubchem Compound ID6262
Kegg IDC01602
ChemSpider ID6026
FOODB IDFDB009998
WikipediaOrnithine
BioCyc IDL-ORNITHINE

Enzymes

Protein Details
1. Arginase
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.
Protein Details
2. Arginine biosynthesis bifunctional protein ArgJ, mitochondrial
General function:
Involved in glutamate N-acetyltransferase activity
Specific function:
Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis:the synthesis of acetylglutamate from glutamate and acetyl-CoA, and of ornithine by transacetylation between acetylornithine and glutamate
Gene Name:
ARG7
Uniprot ID:
Q04728
Molecular weight:
47848.30078
Reactions
N(2)-acetyl-L-ornithine + L-glutamate → L-ornithine + N-acetyl-L-glutamate.
Acetyl-CoA + L-glutamate → CoA + N-acetyl-L-glutamate.
Protein Details
3. Ornithine carbamoyltransferase
General function:
Involved in carboxyl- or carbamoyltransferase activity
Specific function:
Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
Gene Name:
ARG3
Uniprot ID:
P05150
Molecular weight:
37844.80078
Reactions
Carbamoyl phosphate + L-ornithine → phosphate + L-citrulline.
Protein Details
4. Ornithine decarboxylase
General function:
Involved in catalytic activity
Specific function:
L-ornithine = putrescine + CO(2)
Gene Name:
SPE1
Uniprot ID:
P08432
Molecular weight:
52284.80078
Reactions
L-ornithine → putrescine + CO(2).
Protein Details
5. Ornithine aminotransferase
General function:
Involved in transaminase activity
Specific function:
L-ornithine + a 2-oxo acid = L-glutamate 5- semialdehyde + an L-amino acid
Gene Name:
CAR2
Uniprot ID:
P07991
Molecular weight:
46085.60156
Reactions
L-ornithine + a 2-oxo acid → L-glutamate 5-semialdehyde + an L-amino acid.