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Identification
YMDB IDYMDB00060
NameCitrulline
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionCitrulline, also known as Cit or δ-ureidonorvaline, 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. Citrulline is a very strong basic compound (based on its pKa). Citrulline exists in all living species, ranging from bacteria to humans. Citrulline is a potentially toxic compound.
Structure
Thumb
Synonyms
  • (2S)-2-amino-5-(carbamoylamino)pentanoate
  • (2S)-2-amino-5-(carbamoylamino)pentanoic acid
  • (S)-2-amino-5-(aminocarbonyl)aminopentanoate
  • (S)-2-amino-5-(aminocarbonyl)aminopentanoic acid
  • (S)-2-Amino-5-ureidopentanoate
  • (S)-2-Amino-5-ureidopentanoic acid
  • 2-Amino-5-uredovalerate
  • 2-Amino-5-uredovaleric acid
  • 2-Amino-5-ureidovalerate
  • 2-Amino-5-ureidovaleric acid
  • A-amino-d-ureidovalerate
  • A-amino-d-ureidovaleric acid
  • Alpha-amino-delta-ureidovalerate
  • Alpha-amino-delta-ureidovaleric acid
  • Alpha-amino-gamma-ureidovalerate
  • Alpha-amino-gamma-ureidovaleric acid
  • Amino-ureidovalerate
  • Amino-ureidovaleric acid
  • CIR
  • CIT
  • Cytrulline
  • D-ureidonorvaline
  • Delta-ureidonorvaline
  • DL-citrulline
  • Gammaureidonorvaline
  • H-cit-oh
  • L-2-Amino-5-ureido-valerate
  • L-2-Amino-5-ureido-valeric acid
  • L-2-Amino-5-ureidovalerate
  • L-2-Amino-5-ureidovaleric acid
  • L-citrulline
  • L-cytrulline
  • L-N5-carbamoyl-Ornithine
  • L(+)-2-Amino-5-ureidovalerate
  • L(+)-2-Amino-5-ureidovaleric acid
  • L(+)-citrulline
  • N-carbamylornithine
  • N()-carbamylornithine
  • N(5)-(aminocarbonyl)-DL-Ornithine
  • N(delta)-carbamylornithine
  • N5-(aminocarbonyl)ornithine
  • N5-(Aminocarbonyl)-L-ornithine
  • N5-(aminocarbonyl)-Ornithine
  • N5-(Aminocarbonyl)ornithine
  • N5-Carbamoyl-L-ornithine
  • N5-carbamoylornithine
  • N5-carbamylornithine
  • ND-carbamylornithine
  • Ndelta-carbamy-ornithine
  • Ndelta-carbamylornithine
  • Ngamma-carbamylornithine
  • Sitrulline
  • Ureidonorvaline
  • Ureidovalerate
  • Ureidovaleric acid
  • N(5)-(Aminocarbonyl)-L-ornithine
  • a-Amino-delta-ureidovalerate
  • a-Amino-delta-ureidovaleric acid
  • Α-amino-δ-ureidovalerate
  • Α-amino-δ-ureidovaleric acid
  • Δ-ureidonorvaline
  • N(Δ)-carbamylornithine
  • a-Amino-δ-ureidovalerate
  • a-Amino-δ-ureidovaleric acid
CAS number372-75-8
WeightAverage: 175.1857
Monoisotopic: 175.095691297
InChI KeyRHGKLRLOHDJJDR-BYPYZUCNSA-N
InChIInChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1
IUPAC Name(2S)-2-amino-5-(carbamoylamino)pentanoic acid
Traditional IUPAC NameL-citrulline
Chemical FormulaC6H13N3O3
SMILES[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)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
  • Isourea
  • Amino acid
  • Carboximidic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carboximidamide
  • Amine
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Primary aliphatic amine
  • Organopnictogen compound
  • Imine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point235.5 °C
Experimental Properties
PropertyValueReference
Water Solubility212 mg/mL [HMP experimental]PhysProp
LogP-3.19 [SANGSTER (1994)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility21.8 g/LALOGPS
logP-3.3ALOGPS
logP-3.9ChemAxon
logS-0.9ALOGPS
pKa (Strongest Acidic)2.27ChemAxon
pKa (Strongest Basic)9.23ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area118.44 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity41.33 m³·mol⁻¹ChemAxon
Polarizability17.35 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Arginine and proline metabolismec00330 Map00330
SMPDB Reactions
Adenosine triphosphate + Citrulline + L-Aspartic acidPyrophosphate + Adenosine monophosphate + Argininosuccinic acid
KEGG Reactions
L-Aspartic acid + Adenosine triphosphate + CitrullineAdenosine monophosphate + Pyrophosphate + Argininosuccinic acid + hydron
Ornithine + CarbamoylphosphateCitrulline + phosphate + hydron
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
5000 ± 0 µM Minimal medium supplemented with ammonium and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
2000 ± 0 µM Minimal medium supplemented with arginine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0a4i-0920000000-2d92b63cd5d9648023b8JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-00di-9610000000-2e7cd23afc2adcef35a3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4i-0920000000-2d92b63cd5d9648023b8JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00di-9610000000-2e7cd23afc2adcef35a3JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-007o-9100000000-1f8dd2c6648b104639c7JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00dl-9410000000-37909012a777213f8566JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-008a-0904000000-23fbe48f82e515087d68JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-03di-5900000000-78afcbaf8b8b3eabf174JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-001i-0900000000-8fb191d4c20fd54b9282JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-00di-0900000000-da484f0362a8dca5127eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-00e9-0900000000-46229b4f77feabb3f857JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-001i-0900000000-4aca1022c393602a297dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-001i-0900000000-3bc2eff2e907b7734cc8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-001i-3900000000-2613bf40e3be814da86fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9300000000-e83287bbc060eb9cf6f3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-001i-0900000000-daf5b8d935c6f60c6df7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00e9-0900000000-46229b4f77feabb3f857JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-0900000000-4aca1022c393602a297dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-0900000000-322d7f0082e7d5c6ebeeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-3900000000-2613bf40e3be814da86fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-9300000000-e83287bbc060eb9cf6f3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-03di-5900000000-78afcbaf8b8b3eabf174JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-001i-0900000000-8fb191d4c20fd54b9282JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-00di-0900000000-da484f0362a8dca5127eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-001i-0900000000-daf5b8d935c6f60c6df7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001i-0900000000-20fe8593ca8d8303d73aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001i-0900000000-a2851fcef80bb0d9b984JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0a4i-0900000000-4c1d7af748a47e489949JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-988fced362fc0da157c9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-0818e0e8bcee12692498JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-004j-0900000000-5fa8a338dcd2f2a6bdd2JSpectraViewer | MoNA
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
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
  • 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
  • Gancedo, J. M., Gancedo, C. (1973). "Concentrations of intermediary metabolites in yeast." Biochimie 55:205-211.4578278
Synthesis Reference:Kakimoto, Toshio; Shibatani, Takeji; Nishimura, Noriyuki; Chibata, Ichiro. Enzymic production of L-citrulline by Pseudomonas putida. Applied Microbiology (1971), 22(6), 992-9.
External Links:
ResourceLink
CHEBI ID16349
HMDB IDHMDB00904
Pubchem Compound ID9750
Kegg IDC00327
ChemSpider ID9367
FOODB IDFDB011841
WikipediaCitrulline
BioCyc IDL-CITRULLINE

Enzymes

General function:
Involved in argininosuccinate synthase activity
Specific function:
In yeast, as can have a catabolic function since it allows efficient utilization of citrulline via arginine and the reactions involved in the arginase pathway
Gene Name:
ARG1
Uniprot ID:
P22768
Molecular weight:
46939.30078
Reactions
ATP + L-citrulline + L-aspartate → AMP + diphosphate + N(omega)-(L-arginino)succinate.
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.