{"ymdb_id":"YMDB00250","created_at":"2011-05-29T17:58:38.000Z","updated_at":"2016-09-08T18:35:14.000Z","name":"S-adenosyl-4-methylthio-2-oxobutanoic acid","cas":null,"state":null,"melting_point":null,"description":"S-Adenosyl-4-methylthio-2-oxobutanoic acid is a product in the biotin biosynthesis pathway from 7-keto-8-aminopelargonate. [Biocyc PWY0-1507]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"8944","hmdb_id":null,"kegg_id":"C04425","pubchem_id":"440336","cs_id":"24785122","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(3-carboxy-3-oxopropyl)methylsulfanium","traditional_iupac":"{[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(3-carboxy-3-oxopropyl)methylsulfanium","logp":"-3.6261623286390976","pka":"12.44385672367303","alogps_solubility":"9.77e-01 g/l","alogps_logp":"-0.25","alogps_logs":"-2.65","acceptor_count":"10","donor_count":"4","rotatable_bond_count":"7","polar_surface_area":"173.67999999999998","refractivity":"93.71979999999996","polarizability":"38.62888552862654","formal_charge":"1","physiological_charge":"0","pka_strongest_basic":"4.990943331277994","pka_strongest_acidic":"2.749548360954184","bioavailability":"1","number_of_rings":"3","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["(3-carboxy-3-oxopropyl)(5'-deoxyadenosin-5'-yl)(methyl)sulfonium","[1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-carboxylato-3-oxopropyl](methyl)sulfonium","{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(3-carboxy-3-oxopropyl)methylsulfonium","4-[(5'-adenosyl)(methyl)sulfonio]-2-oxobutanoate","4-[(5'-deoxyadenosin-5'-yl)(methyl)sulfonio]-2-oxobutanoate","4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)sulfonio]-2-oxobutanoate","S-Adenosyl-4-methylthio-2-oxobutanoate"],"pathways":[{"name":"Biotin Biosynthesis","kegg_map_id":null}],"growth_conditions":[],"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":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."}],"proteins":[{"created_at":"2011-05-26T19:26:29.000Z","updated_at":"2011-07-22T17:54:00.000Z","name":"Adenosylmethionine-8-amino-7-oxononanoate aminotransferase","uniprot_id":"P50277","uniprot_name":"BIOA_YEAST","enzyme":true,"transporter":false,"gene_name":"BIO3","num_residues":480,"molecular_weight":"53708.39844","theoretical_pi":"6.41","general_function":"Involved in transaminase activity","specific_function":"Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor","reactions":[{"id":1274,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2566,"direction":"\u003e","locations":null,"altext":"S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate.","export":false,"pw_reaction_id":null,"source":null},{"id":3754,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006278","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AB200248","genbank_protein_id":"67772574","gene_card_id":"BIO3","chromosome_location":"chromosome 14","locus":"YNR058W","synonyms":["7,8-diamino-pelargonic acid aminotransferase","DAPA AT","DAPA aminotransferase","Diaminopelargonic acid synthase"],"enzyme_classes":["2.6.1.62"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" cofactor binding"},{"category":"Function","description":" pyridoxal phosphate binding"},{"category":"Function","description":" adenosylmethionine-8-amino-7-oxononanoate transaminase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" transferase activity, transferring nitrogenous groups"},{"category":"Function","description":" transaminase activity"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"},{"category":"Process","description":" biotin metabolic process"},{"category":"Process","description":" biotin biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Aminotran_3","identifier":"PF00202"}],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"name":"Biotin Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGTCCCAAGAAATTTCATATACACCAGATGTCGCGGAACTGCTAGACTTTGATAAAAAACATATTTGGCATCCTTATACGTCATTGAGTTCACCATTGAACGTTTATCCGGTAAAGAGTGCTCACGGATGCAAGCTGGTGTTGGATACCGACTCACCAGTGGACGTCGAGGTGATCGACGCCATGTCGTCGTGGTGGTGTGTTATTCACGGGTACAATAATCCAGAATTAAATGAGGCCCTTACCAAGCAGATGTTAAAGTTTTCTCACGTCCTTCTTGGTGGATTCACCCATAAAGGAGCTGTGAATCTAGTCCAAAAACTTTTAAAAGTGATTGATGAACCCTCTTTGCAGTACTGTTTCCTCGCAGATTCTGGCTCAGTAGCAGTGGAAGTAGCTTTGAAGATGGCTTTACAATCAAACATGTCAGGGGAAGCTACTAAAAATAGAACAAAATTTTTGACAATCAAGAACGGGTATCATGGTGATACATTTGGCGCTATGAGTGTTTGTGATCCTGAGAATTCTATGCATCATATCTACAACGATCGACTCAGTGAGAACATCTTCGCCCAAGCTCCCTCTATTGTCGATGGTCTTCCAACCAGCCAGAACGGTTTCGAGGACCATTGGAATGCAGAAGAAGTTACCGATCTCAAGAAGCAATTTGAATTGCATAGTGATGAGATCTGTGCTGTGATTTTGGAGCCTATCTTACAGGGTGCAGGAGGTTTGCGACCATACCATCCACAGTTCCTAATTGAAGTTCAGAAACTATGTAACCAATACGACGTTTTATTCATCATGGACGAGATTGCTACGGGATTTGGTAGAACAGGTGAGATTTTCGCATTCAAGCACTGTCAAAAATACCAGGACCAACGTGGCATCAGTCCTTCCGATCAGATCAAAGTTGTTCCTGACATATTGTGCGTTGGGAAGGGCTTAACCAGTGGATATATGACTATGAGTGCAGTGGTAGTCAACGACAAAGTTGCTTCCAGAATCTCTTCTCCAAATAGCCCTACTGGTGGCTGCTTCATGCATGGCCCCACCTTCATGGGCAATGCCCTGGCATGCAGTGTGGCAGAAAAGTCTATGGATATACTACTGCGTGGCGAGTGGAGAAAACAAGTGTCTGCAATTGAAGACCAAATTTATAGAGAACTATACCAGTACATCAAGAACCCAGATAATGGGCTCATTGGAACTGTTGTTAAGCGTGTGTCAGTTATTGGAGCTGTAGGTATCGTAGAGCTATACAAGAAGACAGATCCCGAGTGGTTCCAGAAAAAGTTTATATCCAAGGGAGTACATATCCGACCTTTCAACTGCCTGTGTTACATTATGCCACCATATGTGATCACGACAGAGGAATTGACGAAGGTTAATCAAGTCTTGATTGAAGTATTACATGAGTGGAAATCCCACATAAACCAATGA","protein_sequence":"MSQEISYTPDVAELLDFDKKHIWHPYTSLSSPLNVYPVKSAHGCKLVLDTDSPVDVEVIDAMSSWWCVIHGYNNPELNEALTKQMLKFSHVLLGGFTHKGAVNLVQKLLKVIDEPSLQYCFLADSGSVAVEVALKMALQSNMSGEATKNRTKFLTIKNGYHGDTFGAMSVCDPENSMHHIYNDRLSENIFAQAPSIVDGLPTSQNGFEDHWNAEEVTDLKKQFELHSDKICAVILEPILQGAGGLRPYHPQFLIEVQKLCNQYDVLFIMDEIATGFGRTGEIFAFKHCQKYQDQHGISPSDQIKVVPDILCVGKGLTSGYMTMSAVVVNDKVASRISSPNSPTGGCFMHGPTFMGNALACSVAEKSMDILLRGEWRKQVSAIENQIYRELYQYIKNPDNGLIGTVVKRVSVIGAVGIVELYKKTDPEWFQKKFISKGVHIRPFNCLCYIMPPYVITTEELTKVNQVLIEVLHEWKSHINQ"}]}