{"ymdb_id":"YMDB00144","created_at":"2011-05-29T16:01:13.000Z","updated_at":"2016-09-08T18:35:05.000Z","name":"Homoisocitric acid","cas":null,"state":null,"melting_point":null,"description":"Homoisocitric acid is an intermediate in lysine biosynthesis pathway. S. cerevisiae synthesizes the essential amino acid L-lysine via the L-alpha-aminoadipate pathway instead of the diaminopimelate pathway. [Biocyc LYSINE-AMINOAD-PWY]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"Mitochondrion","synthesis_reference":null,"chebi_id":"30903","hmdb_id":null,"kegg_id":"C05662","pubchem_id":"5460287","cs_id":"21865262","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid","traditional_iupac":"(-)-homoisocitric acid","logp":"-1.0017595846666665","pka":"3.9340746844137886","alogps_solubility":"2.62e+01 g/l","alogps_logp":"-0.54","alogps_logs":"-0.90","acceptor_count":"7","donor_count":"4","rotatable_bond_count":"6","polar_surface_area":"132.13","refractivity":"40.3171","polarizability":"17.626131533372334","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"-4.012518164144468","pka_strongest_acidic":"3.12028269600076","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(-)-1-Hydroxy-1,2,4-butanetricarboxylate","(1R,2S)-1-Hydroxybutane-1,2,4-tricarboxylate","1-Hydroxybutane-1,2,4-tricarboxylate","3-Carboxy-2-hydroxyadipate","Homoisocitrate"],"pathways":[{"name":"Lysine biosynthesis","kegg_map_id":"00300"}],"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":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":4284830,"citation":"Strassman, M., Ceci, L. N. (1965). \"Enzymatic formation of alpha-ketoadipic acid from homoisocitric acid.\" J Biol Chem 240:4357-4361."},{"pubmed_id":10714900,"citation":"Zabriskie, T. M., Jackson, M. D. (2000). \"Lysine biosynthesis and metabolism in fungi.\" Nat Prod Rep 17:85-97."}],"proteins":[{"created_at":"2011-05-27T01:52:55.000Z","updated_at":"2011-05-27T15:01:16.000Z","name":"Homoisocitrate dehydrogenase, mitochondrial","uniprot_id":"P40495","uniprot_name":"LYS12_YEAST","enzyme":true,"transporter":false,"gene_name":"LYS12","num_residues":371,"molecular_weight":"40068.60156","theoretical_pi":"8.18","general_function":"Involved in magnesium ion binding","specific_function":"Catalyzes the NAD(+)-dependent conversion of homoisocitrate to alpha-ketoadipate","reactions":[{"id":1638,"direction":"\u003c\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2645,"direction":"\u003e","locations":"Mitochondrion","altext":"(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD(+) = 2-oxoadipate + CO(2) + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":3698,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R003281","source":"Smpdb"},{"id":3698,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R003281","source":"Smpdb"},{"id":4175,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006473","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"Z46728","genbank_protein_id":"577120","gene_card_id":"LYS12","chromosome_location":"chromosome 9","locus":"YIL094C","synonyms":[],"enzyme_classes":["1.1.1.87"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" magnesium ion binding"},{"category":"Function","description":" oxidoreductase activity, acting on CH-OH group of donors"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor"},{"category":"Function","description":" NAD or NADH binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleotide binding"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Iso_dh","identifier":"PF00180"}],"pathways":[{"name":"Lysine biosynthesis","kegg_map_id":"00300"},{"name":"Citric Acid Cycle 1434561204","kegg_map_id":null},{"name":"TCA Cycle","kegg_map_id":null},{"name":"lysine metabolism","kegg_map_id":null}],"gene_sequence":"ATGTTTAGATCTGTTGCTACTAGATTATCTGCCTGCCGTGGGTTAGCATCTAACGCTGCTCGCAAATCACTCACTATTGGTCTTATCCCCGGTGACGGTATCGGTAAGGAAGTCATTCCTGCTGGTAAGCAAGTTTTGGAAAACCTTAACTCCAAGCACGGCCTAAGCTTCAACTTTATTGATCTCTACGCCGGTTTCCAAACATTCCAAGAAACAGGAAAGGCGTTGCCTGATGAGACTGTTAAAGTGTTGAAGGAACAATGTCAAGGTGCTCTTTTCGGTGCAGTTCAGTCTCCAACTACTAAGGTGGAAGGTTACTCCTCACCAATTGTTGCTCTAAGGAGGGAAATGGGCCTTTTCGCTAATGTTCGTCCTGTTAAGTCTGTAGAGGGAGAAAAGGGTAAACCAATTGACATGGTTATCGTCAGAGAAAATACTGAGGACCTGTACATTAAAATTGAAAAAACATACATTGACAAGGCCACAGGTACAAGAGTTGCTGATGCCACAAAGAGAATATCCGAAATTGCAACAAGAAGAATTGCAACCATTGCATTAGATATTGCCTTGAAAAGATTACAAACAAGAGGCCAAGCCACTTTGACAGTGACTCATAAATCAAATGTTCTATCTCAAAGTGATGGTCTATTCAGAGAAATCTGTAAGGAAGTCTACGAATCTAACAAGGACAAGTACGGTCAAATCAAATATAACGAACAAATTGTGGATTCCATGGTTTATAGGCTGTTCAGAGAACCACAATGTTTTGATGTGATAGTGGCACCAAACCTATACGGGGATATATTATCTGACGGTGCTGCTGCTTTAGTCGGTTCATTAGGTGTTGTTCCAAGCGCCAACGTAGGTCCAGAAATTGTCATTGGTGAACCATGCCATGGTTCTGCACCAGATATTGCTGGTAAAGGTATTGCTAACCCAATCGCCACTATAAGATCTACTGCTTTGATGTTGGAATTCTTGGGCCACAACGAAGCTGCCCAAGATATCTACAAGGCTGTTGATGCTAACTTAAGAGAGGGTTCTATCAAGACACCAGATTTAGGTGGTAAGGCTTCTACTCAACAAGTCGTTGACGACGTTTTGTCGAGATTATAG","protein_sequence":"MFRSVATRLSACRGLASNAARKSLTIGLIPGDGIGKEVIPAGKQVLENLNSKHGLSFNFIDLYAGFQTFQETGKALPDETVKVLKEQCQGALFGAVQSPTTKVEGYSSPIVALRREMGLFANVRPVKSVEGEKGKPIDMVIVRENTEDLYIKIEKTYIDKATGTRVADATKRISEIATRRIATIALDIALKRLQTRGQATLTVTHKSNVLSQSDGLFREICKEVYESNKDKYGQIKYNEQIVDSMVYRLFREPQCFDVIVAPNLYGDILSDGAAALVGSLGVVPSANVGPEIVIGEPCHGSAPDIAGKGIANPIATIRSTALMLEFLGHNEAAQDIYKAVDANLREGSIKTPDLGGKASTQQVVDDVLSRL"},{"created_at":"2011-05-27T02:40:18.000Z","updated_at":"2011-07-22T17:53:43.000Z","name":"Homoaconitase, mitochondrial","uniprot_id":"P49367","uniprot_name":"LYS4_YEAST","enzyme":true,"transporter":false,"gene_name":"LYS4","num_residues":693,"molecular_weight":"75150.10156","theoretical_pi":"7.41","general_function":"Involved in metabolic process","specific_function":"Responsible for the dehydration of cis-homoaconitate to homoisocitric acid","reactions":[{"id":1150,"direction":"\u003c\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1635,"direction":"\u003c\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2684,"direction":"\u003e","locations":"Mitochondrion","altext":"(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H(2)O.","export":false,"pw_reaction_id":null,"source":null},{"id":3708,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R003288","source":"Smpdb"},{"id":3709,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R003289","source":"Smpdb"},{"id":4174,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006472","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"AY723781","genbank_protein_id":"51830249","gene_card_id":"LYS4","chromosome_location":"chromosome 4","locus":"YDR234W","synonyms":["Homoaconitate hydratase"],"enzyme_classes":["4.2.1.36"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" metal cluster binding"},{"category":"Function","description":" iron-sulfur cluster binding"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" 4 iron, 4 sulfur cluster binding"},{"category":"Function","description":" homoaconitate hydratase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"},{"category":"Process","description":" aspartate family amino acid metabolic process"},{"category":"Process","description":" lysine metabolic process"},{"category":"Process","description":" lysine biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"}],"pfams":[{"name":"Aconitase","identifier":"PF00330"},{"name":"Aconitase_C","identifier":"PF00694"}],"pathways":[{"name":"Lysine biosynthesis","kegg_map_id":"00300"},{"name":"lysine metabolism","kegg_map_id":null}],"gene_sequence":"ATGCTACGATCAACCACATTTACTCGTTCGTTCCACAGTTCTAGGGCCTGGTTGAAAGGTCAGAACCTAACTGAAAAAATTGTTCAGTCGTATGCGGTCAACCTTCCCGAGGGTAAAGTTGTGCATTCTGGTGACTATGTATCGATCAAGCCGGCACACTGTATGTCCCACGATAATTCGTGGCCTGTAGCTTTGAAATTCATGGGGCTTGGCGCTACCAAGATCAAGAATCCTTCACAGATTGTGACCACTCTGGACCACGATATTCAGAACAAATCAGAGAAAAATTTGACCAAGTACAAGAACATCGAAAATTTTGCTAAGAAACACCATATAGACCACTACCCTGCCGGTAGAGGTATTGGTCATCAAATTATGATTGAGGAGGGCTATGCTTTCCCCTTGAACATGACTGTCGCATCTGACTCGCATTCAAACACCTACGGTGGTCTGGGGTCGCTGGGCACTCCAATAGTGAGAACAGACGCTGCAGCCATATGGGCCACGGGACAGACGTGGTGGCAGATCCCACCAGTGGCTCAGGTTGAGTTGAAAGGTCAATTGCCTCAGGGTGTTTCCGGAAAAGATATCATTGTCGCATTATGTGGGCTTTTCAACAATGATCAAGTTCTAAATCACGCCATTGAATTCACGGGTGACTCTTTGAATGCATTGCCTATCGATCACAGACTCACTATTGCTAACATGACCACCGAGTGGGGGGCTCTTTCTGGTTTGTTCCCCGTGGACAAAACTTTGATCGACTGGTATAAAAACCGTTTGCAAAAGCTGGGCACCAATAATCATCCAAGGATTAATCCAAAGACTATCCGCGCACTAGAAGAAAAGGCGAAGATTCCGAAAGCAGACAAGGATGCACATTATGCCAAGAAACTGATCATCGATCTAGCCACGCTAACTCACTACGTCTCAGGTCCAAATAGTGTTAAGGTCTCCAACACCGTGCAAGATCTATCTCAACAAGACATCAAGATAAATAAAGCTTATCTAGTGTCATGTACAAACTCCCGTCTATCTGATTTGCAATCTGCAGCGGATGTGGTTTGTCCTACTGGAGACTTAAACAAAGTCAACAAGGTGGCTCCAGGTGTGGAGTTCTATGTCGCTGCTGCCTCTTCAGAAATTGAGGCTGATGCCCGTAAATCAGGCGCTTGGGAAAAGCTGCTAAAGGCTGGCTGTATCCCACTGCCTTCTGGTTGTGGTCCATGCATCGGTCTAGGTGCGGGATTACTGGAACCAGGTGAAGTTGGTATCAGTGCCACAAACAGAAACTTCAAAGGTAGAATGGGTTCCAAGGATGCATTGGCTTACTTAGCTTCCCCTGCTGTAGTCGCCGCTTCTGCCGTGCTGGGTAAGATTAGTTCTCCTGCTGAGGTATTGTCCACAAGCGAAATTCCATTCAGCGGCGTTAAGACTGAGATAATTGAGAATCCCGTGGTTGAAGAGGAAGTTAACGCTCAAACAGAGGCTCCAAAACAATCCGTTGAGATATTAGAAGGTTTCCCAAGAGAGTTTTCTGGTGAATTAGTTTTATGTGATGCCGATAACATCAATACCGATGGTATATATCCTGGTAAGTACACTTATCAGGATGATGTGCCTAAAGAAAAGATGGCGCAAGTTTGTATGGAAAATTATGATGCCGAGTTCAGAACCAAGGTTCATCCAGGTGATATAGTGGTCAGTGGGTTCAATTTCGGTACCGGTTCCTCCAGGGAACGAGCGGCCACCGCCTTATTGGCTAAAGGTATCAACTTAGTTGTTTCAGGATCTTTTGGTAATATTTTTTCAAGAAACTCCATTAACAATGCTCTTCTGACCTTGGAAATCCCAGCATTAATCAAAAAATTACGTGAGAAATATCAAGGTGCTCCAAAAGAACTTACAAGAAGAACTGGTTGGTTTTTGAAATGGGATGTAGCTGATGCTAAAGTGGTCGTTACCGAAGGTTCTTTGGACGGCCCTGTGATCTTGGAGCAAAAAGTGGGTGAGCTAGGTAAGAACCTACAAGAAATTATTGTAAAAGGAGGCTTGGAAGGTTGGGTCAAATCCCAACTATAA","protein_sequence":"MLRSTTFTRSFHSSRAWLKGQNLTEKIVQSYAVNLPEGKVVHSGDYVSIKPAHCMSHDNSWPVALKFMGLGATKIKNPSQIVTTLDHDIQNKSEKNLTKYKNIENFAKKHHIDHYPAGRGIGHQIMIEEGYAFPLNMTVASDSHSNTYGGLGSLGTPIVRTDAAAIWATGQTWWQIPPVAQVELKGQLPQGVSGKDIIVALCGLFNNDQVLNHAIEFTGDSLNALPIDHRLTIANMTTEWGALSGLFPVDKTLIDWYKNRLQKLGTNNHPRINPKTIRALEEKAKIPKADKDAHYAKKLIIDLATLTHYVSGPNSVKVSNTVQDLSQQDIKINKAYLVSCTNSRLSDLQSAADVVCPTGDLNKVNKVAPGVEFYVAAASSEIEADARKSGAWEKLLKAGCIPLPSGCGPCIGLGAGLLEPGEVGISATNRNFKGRMGSKDALAYLASPAVVAASAVLGKISSPAEVLSTSEIPFSGVKTEIIENPVVEEEVNAQTEAPKQSVEILEGFPREFSGELVLCDADNINTDGIYPGKYTYQDDVPKEKMAQVCMENYDAEFRTKVHPGDIVVSGFNFGTGSSREQAATALLAKGINLVVSGSFGNIFSRNSINNALLTLEIPALIKKLREKYQGAPKELTRRTGWFLKWDVADAKVVVTEGSLDGPVILEQKVGELGKNLQEIIVKGGLEGWVKSQL"}]}