{"ymdb_id":"YMDB00060","created_at":"2011-05-29T15:52:55.000Z","updated_at":"2016-10-18T17:11:16.000Z","name":"Citrulline","cas":"372-75-8","state":"Solid","melting_point":"235.5 oC","description":"Citrulline is a non-proteinogenic amino acid made from ornithine and carbamoyl phosphate in one of the central reactions in the urea cycle. It is also produced from arginine as a by-product of the reaction catalyzed by NOS family [EC 1.14.13.39].","experimental_water_solubility":"212 mg/mL [HMP experimental]","experimental_logp_hydrophobicity":"-3.19 [SANGSTER (1994)]","location":"cytoplasm","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.","chebi_id":"16349","hmdb_id":"HMDB00904","kegg_id":"C00327","pubchem_id":"9750","cs_id":"9367","foodb_id":null,"wikipedia_link":"Citrulline","biocyc_id":"L-CITRULLINE","iupac":"(2S)-2-amino-5-(carbamoylamino)pentanoic acid","traditional_iupac":"L-citrulline","logp":"-3.9319578381140263","pka":"15.333969157335531","alogps_solubility":"2.18e+01 g/l","alogps_logp":"-3.27","alogps_logs":"-0.90","acceptor_count":"4","donor_count":"4","rotatable_bond_count":"5","polar_surface_area":"118.43999999999998","refractivity":"41.329","polarizability":"17.34757818367823","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"9.225134668659093","pka_strongest_acidic":"2.2682474980163243","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","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","N\u003cSUP\u003e5\u003c/SUP\u003e-(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"],"pathways":[{"name":"Arginine and proline metabolism","kegg_map_id":"00330"}],"growth_conditions":[{"growth_media":"Minimal medium  supplemented with ammonium and glucose","concentration":"5000.0","concentration_units":"\u0026#181;M","error":"0.0"},{"growth_media":"Minimal medium  supplemented with arginine and glucose","concentration":"2000.0","concentration_units":"\u0026#181;M","error":"0.0"}],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."},{"pubmed_id":21062828,"citation":"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."},{"pubmed_id":18846089,"citation":"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."},{"pubmed_id":11553611,"citation":"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."},{"pubmed_id":6370999,"citation":"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."},{"pubmed_id":4578278,"citation":"Gancedo, J. M., Gancedo, C. (1973). \"Concentrations of intermediary metabolites in yeast.\" Biochimie 55:205-211."}],"proteins":[{"created_at":"2011-05-26T16:43:33.000Z","updated_at":"2011-07-22T17:54:12.000Z","name":"Argininosuccinate synthase","uniprot_id":"P22768","uniprot_name":"ASSY_YEAST","enzyme":true,"transporter":false,"gene_name":"ARG1","num_residues":420,"molecular_weight":"46939.30078","theoretical_pi":"5.4","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","reactions":[{"id":1328,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2440,"direction":"\u003e","locations":null,"altext":"ATP + L-citrulline + L-aspartate = AMP + diphosphate + N(omega)-(L-arginino)succinate.","export":false,"pw_reaction_id":null,"source":null},{"id":3736,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006261","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"M35237","genbank_protein_id":"171085","gene_card_id":"ARG1","chromosome_location":"chromosome 15","locus":"YOL058W","synonyms":["Citrulline--aspartate ligase"],"enzyme_classes":["6.3.4.5"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" argininosuccinate synthase activity"},{"category":"Function","description":" ligase activity"},{"category":"Function","description":" ligase activity, forming carbon-nitrogen bonds"},{"category":"Process","description":" cellular amino acid metabolic process"},{"category":"Process","description":" glutamine family amino acid metabolic process"},{"category":"Process","description":" arginine metabolic process"},{"category":"Process","description":" arginine biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"}],"pfams":[{"name":"Arginosuc_synth","identifier":"PF00764"}],"pathways":[{"name":"Alanine, aspartate and glutamate metabolism","kegg_map_id":"00250"},{"name":"Arginine and proline metabolism","kegg_map_id":"00330"}],"gene_sequence":"ATGTCTAAGGGAAAAGTTTGTTTGGCTTATTCTGGTGGTTTAGATACCTCCGTCATTTTGGCTTGGCTACTAGACCAGGCTACGGAAGTTGTAGCTTTCATGGCTAATGTAGGGCAAGAAGAAGATTTCGATGCCGCCAAGGTTTTGGCCTTGAAGATCGGTGCCTGCAAGTTCGTTTGTGGTGGATTGTCTGAAGATTTTGTCAAGGATATTCTATTCCCAGCTGTACAGGTCAACGCTGTGTACGAAGACGTTTATCTGTTGGGTACCTCTTTGGCAAGACCTGTTATTGCCAAAGCCCAAATTGACGTCGCTAAACAGGAGGGCTGTTTCGCGGTCTCTCATGGTTGTACCGGCAAAGGTAATGATCAAATCAGATTCGAATTGTCATTTTACGCTCTGAAGCCAGACGTTAAGTGTATTACACCATGGAGAATGCCTGAATTTTTCGAAAGATTTGCTGGCAGAAAGGATTTGTTAGACTATGCTGCACAAAAGGGTATTTTTGTCGCCCAAACCAAGGCCAAGCCATGGTCTACTGACGAAAACCAAGCCCACATTTCTTACGAGGCAGGTATCTTGGAAGACCCAGATACCACCCCACCAAAGGACATGTGGAAATTGATCGTCGATCCAATGGATGCTCCGGACCAACCACAAGATTTGACCATTGACTTTGAACGTGGTCTTCCAGTCAAGTTGACCTACACCGACAACAAGACTTCCAAGGAAGTTTCCGTTACCAAGCCTTTGGATGTTTTCTTGGCCGCATCCAACTTAGCAAGGGCCAACGGTGTTGGTAGAATCGATATTGTAGAAGATCGTTACATTAACTTGAAATCCAGAGGTTGTTACGAACAGGCTCCATTGACTGTTTTGAGAAAAGCTCATGTTGATTTGGAAGGTTTGACTTTAGACAAAGAAGTCCGTCAATTGAGAGACTCATTGGTCACTCCAAACTACTCCAGATTGATATATAACGGTTTCCTACTTCACCCAGAGTGTGAGTACATCAGATCTATGATCCAACCATCCCAAAATAGCGTTAACGGTACTGTCAGGGTTAGACTGTATAAGGGTAACGTCATCATTCTGGGCAGATCTACAAAGACTGAAAAGTTGTACGATCCGACAGAATCCTCTATGGATGAGTTGACCGGTTTCTTACCTACCGATACCACCGGTTTCATTGCCATCCAGGCCATTAGAATTAAAAAATACGGTGAATCCAAAAAAACCAAAGGTGAAGAGTTGACTTTGTAA","protein_sequence":"MSKGKVCLAYSGGLDTSVILAWLLDQGYEVVAFMANVGQEEDFDAAKEKALKIGACKFVCVDCREDFVKDILFPAVQVNAVYEDVYLLGTSLARPVIAKAQIDVAKQEGCFAVSHGCTGKGNDQIRFELSFYALKPDVKCITPWRMPEFFERFAGRKDLLDYAAQKGIPVAQTKAKPWSTDENQAHISYEAGILEDPDTTPPKDMWKLIVDPMDAPDQPQDLTIDFERGLPVKLTYTDNKTSKEVSVTKPLDVFLAASNLARANGVGRIDIVEDRYINLKSRGCYEQAPLTVLRKAHVDLEGLTLDKEVRQLRDSFVTPNYSRLIYNGFLLHPECEYIRSMIQPSQNSVNGTVRVRLYKGNVIILGRSTKTEKLYDPTESSMDELTGFLPTDTTGFIAIQAIRIKKYGESKKTKGEELTL"},{"created_at":"2011-05-26T16:52:31.000Z","updated_at":"2011-05-27T15:01:01.000Z","name":"Ornithine carbamoyltransferase","uniprot_id":"P05150","uniprot_name":"OTC_YEAST","enzyme":true,"transporter":false,"gene_name":"ARG3","num_residues":338,"molecular_weight":"37844.80078","theoretical_pi":"6.24","general_function":"Involved in carboxyl- or carbamoyltransferase activity","specific_function":"Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline","reactions":[{"id":1804,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2450,"direction":"\u003e","locations":"Cytoplasm","altext":"Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"M11946","genbank_protein_id":"171075","gene_card_id":"ARG3","chromosome_location":"chromosome 10","locus":"YJL088W","synonyms":["Ornithine transcarbamylase","OTCase"],"enzyme_classes":["2.1.3.3"],"go_classes":[{"category":"Component","description":" macromolecular complex"},{"category":"Component","description":" protein complex"},{"category":"Component","description":" ornithine carbamoyltransferase complex"},{"category":"Function","description":" binding"},{"category":"Function","description":" carboxylic acid binding"},{"category":"Function","description":" amino acid binding"},{"category":"Function","description":" carboxyl- or carbamoyltransferase activity"},{"category":"Function","description":" ornithine carbamoyltransferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring one-carbon groups"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"}],"pfams":[{"name":"OTCace","identifier":"PF00185"},{"name":"OTCace_N","identifier":"PF02729"}],"pathways":[{"name":"Arginine and proline metabolism","kegg_map_id":"00330"}],"gene_sequence":"ATGTCAACCACAGCATCCACGCCTTCATCTTTACGTCATTTGATTTCTATAAAAGATCTTTCTGATGAAGAATTCAGAATCTTAGTACAAAGAGCTCAACATTTCAAGAATGTTTTTAAAGCAAATAAAACGAATGATTTCCAATCCAACCATCTGAAACTATTGGGTAGAACTATAGCCTTAATATTTACTAAAAGATCAACTAGAACGAGAATTTCGACCGAAGGTGCAGCCACCTTCTTTGGTGCCCAACCGATGTTTTTAGGTAAAGAGGATATTCAGCTTGGTGTCAATGAATCATTTTACGATACCACCAAGGTTGTATCATCTATGGTTTCATGTATTTTTGCCCGTGTGAACAAACATGAAGACATACTTGCTTTTTGCAAGGATTCCTCTGTACCGATCATCAACTCTCTATGTGACAAATTCCACCCTTTGCAAGCAATTTGTGATCTTTTAACAATAATCGAAAACTTCAATATATCTCTAGATGAAGTAAATAAGGGAATCAATTCAAAATTGAAGATGGCATGGATTGGTGATGCCAATAATGTCATAAATGATATGTGCATCGCATGTCTGAAATTCGGTATAAGTGTCAGTATTTCCACTCCCCCCGGTATTGAAATGGATTCCGATATTGTCGATGAAGCAAAGAAAGTTGCTGAGAGAAACGGTGCGACATTTGAATTAACACACGACTCTTTAAAGGCCTCCACCAATGCCAATATATTAGTAACCGATACTTTCGTTTCCATGGGTGAAGAATTTGCGAAACAGGCCAAGCTGAAACAATTCAAAGGTTTTCAAATCAATCAAGAACTTGTCTCTGTGGCTGATCCAAACTACAAATTTATGCATTGTCTGCCAAGACATCAAGAAGAAGTTAGTGATGATGTCTTTTATGGAGAGCATTCCATAGTCTTTGAAGAAGCAGAAAACAGATTATATGCAGCTATGTCTGCCATTGATATCTTTGTTAATAATAAAGGTAATTTCAAGGACTTGAAATAA","protein_sequence":"MSTTASTPSSLRHLISIKDLSDEEFRILVQRAQHFKNVFKANKTNDFQSNHLKLLGRTIALIFTKRSTRTRISTEGAATFFGAQPMFLGKEDIQLGVNESFYDTTKVVSSMVSCIFARVNKHEDILAFCKDSSVPIINSLCDKFHPLQAICDLLTIIENFNISLDEVNKGINSKLKMAWIGDANNVINDMCIACLKFGISVSISTPPGIEMDSDIVDEAKKVAERNGATFELTHDSLKASTNANILVTDTFVSMGEEFAKQAKLKQFKGFQINQELVSVADPNYKFMHCLPRHQEEVSDDVFYGEHSIVFEEAENRLYAAMSAIDIFVNNKGNFKDLK"}]}