{"ymdb_id":"YMDB00075","created_at":"2011-05-29T15:54:13.000Z","updated_at":"2016-09-08T18:34:59.000Z","name":"Dethiobiotin","cas":"533-48-2","state":"Solid","melting_point":"157 oC","description":"Dethiobiotin is an intermediate in biotin biosynthesis from 7-keto-8-aminopelargonate pathway. Biotin is a water soluble, heterocyclic cofactor for a small number of enzymes that facilitate the transfer of CO2 during carboxylation, decarboxylation, and transcarboxylation reactions involved in fatty acid and carbohydrate metabolism. Biotin biosynthesis is found in plants, bacteria, and certain fungi. [Biocyc PWY0-1507]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"Cytoplasm","synthesis_reference":"Kuzuhara, Hiroyoshi; Ohrui, Hiroshi; Emoto, Sakae.  Syntheses with azido sugars.  II.  Conversion of D-glucose to (+)-dethiobiotin.    Agricultural and Biological Chemistry  (1971),  35(1),  8-17.","chebi_id":"42280","hmdb_id":"HMDB03581","kegg_id":"C01909","pubchem_id":"643","cs_id":"24785644","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid","traditional_iupac":"(4R,5S)-dethiobiotin","logp":"0.7256986656666673","pka":"13.825802330845217","alogps_solubility":"1.27e+00 g/l","alogps_logp":"0.72","alogps_logs":"-2.23","acceptor_count":"3","donor_count":"3","rotatable_bond_count":"6","polar_surface_area":"78.43","refractivity":"54.398","polarizability":"23.15226202416082","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"-1.7681297551220103","pka_strongest_acidic":"4.634655499494166","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"1","veber_rule":"0","mddr_like_rule":"0","synonyms":["Desthiobiotin"],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"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."},{"pubmed_id":17259550,"citation":"Muhlenhoff, U., Gerl, M. J., Flauger, B., Pirner, H. M., Balser, S., Richhardt, N., Lill, R., Stolz, J. (2007). \"The ISC [corrected] proteins Isa1 and Isa2 are required for the function but not for the de novo synthesis of the Fe/S clusters of biotin synthase in Saccharomyces cerevisiae.\" Eukaryot Cell 6:495-504."},{"pubmed_id":16269718,"citation":"Wu, H., Ito, K., Shimoi, H. (2005). \"Identification and characterization of a novel biotin biosynthesis gene in Saccharomyces cerevisiae.\" Appl Environ Microbiol 71:6845-6855."}],"proteins":[{"created_at":"2011-05-26T17:19:36.000Z","updated_at":"2011-07-22T17:54:19.000Z","name":"Biotin synthase, mitochondrial","uniprot_id":"P32451","uniprot_name":"BIOB_YEAST","enzyme":true,"transporter":false,"gene_name":"BIO2","num_residues":375,"molecular_weight":"41883.80078","theoretical_pi":"8.66","general_function":"Involved in catalytic activity","specific_function":"Dethiobiotin + sulfur + 2 S-adenosyl-L- methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine","reactions":[{"id":1347,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2472,"direction":"\u003e","locations":"Mitochondrion","altext":"Dethiobiotin + sulfur + 2 S-adenosyl-L-methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine.","export":false,"pw_reaction_id":null,"source":null},{"id":3756,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006280","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"Z73071","genbank_protein_id":"1323523","gene_card_id":"BIO2","chromosome_location":"chromosome 7","locus":"YGR286C","synonyms":[],"enzyme_classes":["2.8.1.6"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" metal cluster binding"},{"category":"Function","description":" iron-sulfur cluster binding"},{"category":"Function","description":" transferase activity, transferring sulfur-containing groups"},{"category":"Function","description":" sulfurtransferase activity"},{"category":"Function","description":" biotin synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" cofactor 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"}],"pfams":[{"name":"Radical_SAM","identifier":"PF04055"},{"name":"BATS","identifier":"PF06968"}],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"name":"Biotin Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGATGTCTACTATCTACCGTCATTTATCTACCGCTAGACCGGCTTTAACTAAATACGCAACCAATGCCGCAGTTAAATCGACAACTGCATCCTCAGAAGCTAGTACTCTGGGTGCTCTACAATATGCATTGTCTTTAGATGAACCAAGTCATTCGTGGACAAAATCGCAATTAAAAGAAATTTATCATACCCCACTGCTCGAACTTACTCATGCAGCACAATTGCAGCACAGAAAGTGGCACGATCCAACCAAAGTGCAATTGTGCACATTGATGAACATCAAATCTGGTGGTTGTTCTGAGGACTGTAAGTATTGTGCGCAGTCTTCGAGAAACGATACCGGTCTAAAGGCTGAGAAAATGGTTAAAGTGGATGAAGTGATTAAAGAGGCAGAAGAGGCCAAAAGAAACGGATCTACTAGATTCTGCCTAGGTGCTGCATGGAGAGACATGAAAGGTCGTAAATCAGCCATGAAAAGAATTCAGGAAATGGTGACCAAAGTGAATGATATGGGGCTAGAAACGTGTGTTACTTTAGGTATGGTTGATCAAGATCAAGCAAAGCAATTGAAAGATGCAGGTTTGACTGCATACAACCATAACATCGACACTTCCAGAGAACACTATAGTAAGGTCATCACCACGAGAACCTACGACGACAGGTTACAGACCATCAAGAATGTCCAAGAATCTGGAATAAAAGCCTGTACCGGTGGTATTTTGGGTCTCGGTGAAAGCGAAGACGACCATATAGGATTCATCTACACATTATCCAATATGTCTCCTCATCCTGAGTCCCTACCAATTAATAGACTAGTTGCTATCAAAGGGACTCCAATGGCTGAGGAACTTGCCGATCCAAAGAGTAAAAAGTTGCAATTCGACGAAATTTTGAGAACCATTGCCACAGCGAGAATAGTTATGCCAAAGGCCATTATAAGACTTGCCGCTGGTCGTTATACAATGAAAGAAACAGAGCAATTTGTCTGTTTCATGGCAGGTTGTAACAGTATCTTCACCGGTAAGAAAATGCTGACGACAATGTGTAACGGTTGGGACGAAGACAAGGCAATGTTGGCTAAATGGGGATTGCAACCTATGGAGGCATTTAAGTACGACAGATCTTGA","protein_sequence":"MMSTIYRHLSTARPALTKYATNAAVKSTTASSEASTLGALQYALSLDEPSHSWTKSQLKEIYHTPLLELTHAAQLQHRKWHDPTKVQLCTLMNIKSGGCSEDCKYCAQSSRNDTGLKAEKMVKVDEVIKEAEEAKRNGSTRFCLGAAWRDMKGRKSAMKRIQEMVTKVNDMGLETCVTLGMVDQDQAKQLKDAGLTAYNHNIDTSREHYSKVITTRTYDDRLQTIKNVQESGIKACTGGILGLGESEDDHIGFIYTLSNMSPHPESLPINRLVAIKGTPMAEELADPKSKKLQFDEILRTIATARIVMPKAIIRLAAGRYTMKETEQFVCFMAGCNSIFTGKKMLTTMCNGWDEDKAMLAKWGLQPMEAFKYDRS"},{"created_at":"2011-05-26T17:20:03.000Z","updated_at":"2011-07-22T17:54:36.000Z","name":"Dethiobiotin synthetase","uniprot_id":"P53630","uniprot_name":"BIOD_YEAST","enzyme":true,"transporter":false,"gene_name":"BIO4","num_residues":237,"molecular_weight":"26256.69922","theoretical_pi":"4.79","general_function":"Involved in magnesium ion binding","specific_function":"ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin","reactions":[{"id":1449,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2473,"direction":"\u003e","locations":null,"altext":"ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin.","export":false,"pw_reaction_id":null,"source":null},{"id":3755,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006279","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY558424","genbank_protein_id":"45270738","gene_card_id":"BIO4","chromosome_location":"chromosome 14","locus":"YNR057C","synonyms":["DTB synthetase","Dethiobiotin synthase","DTBS"],"enzyme_classes":["6.3.3.3"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" ligase activity"},{"category":"Function","description":" ligase activity, forming carbon-nitrogen bonds"},{"category":"Function","description":" binding"},{"category":"Function","description":" dethiobiotin synthase activity"},{"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":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" magnesium ion binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" cyclo-ligase activity"},{"category":"Process","description":" 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":" small molecule metabolic process"}],"pfams":[],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"name":"Biotin Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGAACAGCAAATCTCAACAACAAGAACAACAACCAATTGTATTCGTCACCGGTACAGACACTGATGTTGGTAAAACCTTTGTATCAACATTATTGGTACACAAATGGAAAGCTGCATACTGGAAACCCGTACAAACTGGAATTGAGTCAGATCAAGGTGACTCCGAGACATTGAAAAATTTCAAAATAGCCGCATCAACTTGGCAACCACCTATATTCACGCCCACTTATGCGCTGCAGAAGCCTCTATCTCCGCTCCAGGCCATGGAGTACGAACCTAATGTCGACATCAGGTTGTTGGATTTCGTAGTTCCTGAAGAGTGGAGCGCAGAGAATCCATTGGTCGTAGAAGGAGCCGGCGGGGTTTGCGTTCCTATCACTCGTAAATTGGAAATTACGACGGATCTAATTAAACATCTGATTGAGACTAGCGGCCATCCAGTGTACGTAGTTGTCGTGGCACGCAGCGGGCTAGGGACTCTGAATCATACATTGCTGACTTGGAATCATCTTTGCGATAATGGCTTGAGAAGCCACCTTTTTGGGGTCATTCTCAATGGGGAACCGAATGAAGGCAACGTGCAGGCCCTGAAGAAGTTCGGTGTCAATATTATGGCACAGGTTGCACAATGTACTACGGCACATGATCAGGATATGGAGTTGCATGAACTGCCATCGGTGGAGTCATTAATGACCCAACAAGACGTAGAATAG","protein_sequence":"MNSKSQQQEQQPIVFVTGTDTDVGKTFVSTLLVHKWKAAYWKPVQTGIESDQGDSETLKNFKIAASTWQPPIFTPTYALQKPLSPLQAMEYEPNVDIRLLDFVVPEEWSAENPLVVEGAGGVCVPITRKLEITTDLIKHLIETSGHPVYVVVVARSGLGTLNHTLLTWNHLCDNGLRSHLFGVILNGEPNEGNVQALKKFGVNIMAQVAQCTTAHDQDMELHELPSVESLMTQQDVE"}]}