{"ymdb_id":"YMDB00340","created_at":"2011-05-29T18:07:41.000Z","updated_at":"2016-09-08T18:35:22.000Z","name":"trans-Aconitic acid","cas":"585-84-2","state":"Solid","melting_point":"125 oC","description":"Aconitic acid is an organic acid. The two isomers are cis-aconitic acid and trans-aconitic acid. The conjugate base of cis-aconitic acid, cis-aconitate is an intermediate in the isomerization of citrate to isocitrate in the citric acid cycle. It is acted upon by the enzyme aconitase.","experimental_water_solubility":"472.5 mg/mL [HMP experimental]","experimental_logp_hydrophobicity":"","location":"mitochondrion;cytoplasm","synthesis_reference":"Gutierrez, Eddie N.; Lamberti, Vincent.  Preparation of aconitic acid.    U.S.  (1978),     5 pp.  CODEN: USXXAM  US  4123459  19781031  CAN 90:103423  AN 1979:103423","chebi_id":"32805","hmdb_id":"HMDB00072","kegg_id":"C02341","pubchem_id":"444212","cs_id":null,"foodb_id":null,"wikipedia_link":"Aconitate","biocyc_id":"CIS-ACONITATE","iupac":"(1E)-prop-1-ene-1,2,3-tricarboxylic acid","traditional_iupac":"trans aconitic acid","logp":"-0.521036942","pka":"3.787966109115829","alogps_solubility":"6.72e+00 g/l","alogps_logp":"-0.41","alogps_logs":"-1.41","acceptor_count":"6","donor_count":"3","rotatable_bond_count":"4","polar_surface_area":"111.9","refractivity":"35.2305","polarizability":"13.9564343716318","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":null,"pka_strongest_acidic":"3.145216334617251","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(1E)-1-propene-1,2,3-tricarboxylic acid","(1E)-Prop-1-ene-1,2,3-tricarboxylic","(1E)1-Propene-1,2,3-tricarboxylate","(1E)1-Propene-1,2,3-tricarboxylic acid","(E)-1-propene-1,2,3-tricarboxylic acid","(E)-Aconitic acid","1-Propene-1-trans-2,3-tricarboxylic acid","1-trans-Propene-1,2,3-tricarboxylic acid","ACONITATE ION","TRA","trans-1-Propene-1,2,3-tricarboxylic acid","trans-Aconitate","trans-Aconitic acid","trans-Propene-1,2,3-tricarboxylic acid"],"pathways":[],"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":19889834,"citation":"Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). \"Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.\" Mol Biol Cell 21:198-211."},{"pubmed_id":15147181,"citation":"Katz, J. E., Dumlao, D. S., Wasserman, J. I., Lansdown, M. G., Jung, M. E., Faull, K. F., Clarke, S. (2004). \"3-Isopropylmalate is the major endogenous substrate of the Saccharomyces cerevisiae trans-aconitate methyltransferase.\" Biochemistry 43:5976-5986."}],"proteins":[{"created_at":"2011-05-27T02:13:35.000Z","updated_at":"2011-07-22T17:53:47.000Z","name":"Trans-aconitate 3-methyltransferase","uniprot_id":"P32643","uniprot_name":"TMT1_YEAST","enzyme":true,"transporter":false,"gene_name":"TMT1","num_residues":299,"molecular_weight":"34768.0","theoretical_pi":"6.18","general_function":"Involved in methyltransferase activity","specific_function":"Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate and 3-isopropylmalate at high affinity and of other molecules like cis-aconitate, isocitrate, and citrate at lower velocities and affinities. The function of trans-aconitate methylation appears to be in reducing the toxicity of this spontaneous breakdown product of cis-aconitate. The role of 3-isopropylmalate methylation is unclear but may represent a metabolic branch at 3-isopropylmalate, where some of the material is taken in the pathway leading to leucine and some is taken in a pathway to the 3-isopropylmalate methyl ester, a molecule that provides a signal to switch from vegetative to invasive growth in response to amino acid starvation","reactions":[{"id":1181,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2014,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2663,"direction":"\u003e","locations":"Cytoplasm","altext":"S-adenosyl-L-methionine + trans-aconitate = S-adenosyl-L-homocysteine + (E)-2-(methoxycarbonylmethyl)butenedioate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"U18922","genbank_protein_id":"603416","gene_card_id":"TMT1","chromosome_location":"chromosome 5","locus":"YER175C","synonyms":[],"enzyme_classes":["2.1.1.145"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring one-carbon groups"},{"category":"Function","description":" methyltransferase activity"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Methyltransf_11","identifier":"PF08241"}],"pathways":[],"gene_sequence":"ATGTCTACCTTTTCTGCTTCTGATTTCAACTCAGAAAGATATTCATCTTCAAGACCTTCTTATCCCTCCGATTTTTACAAGATGATTGATGAATACCACGACGGAGAAAGGAAATTACTCGTAGATGTTGGCTGTGGACCAGGTACTGCCACTTTACAAATGGCTCAGGAGTTAAAACCATTCGAACAAATTATCGGAAGCGATCTCTCCGCTACCATGATTAAGACTGCAGAAGTAATAAAGGAAGGAAGTCCTGATACATACAAAAACGTTTCATTTAAGATTTCTTCAAGTGATGATTTTAAATTCCTAGGCGCGGATTCAGTAGACAAACAGAAAATTGATATGATTACCGCAGTAGAATGTGCTCATTGGTTCGATTTCGAAAAATTTCAGCGATCTGCTTATGCCAATTTGAGAAAAGATGGTACTATCGCTATTTGGGGTTATGCGGACCCAATTTTCCCGGACTACCCTGAATTTGATGATCTGATGATTGAAGTTCCTTACGGGAAGCAAGGACTGGGACCCTATTGGGAACAACCGGGGAGATCTCGCCTTCGTAATATGCTGAAAGACTCTCACTTAGACCCAGAACTTTTCCATGATATACAAGTTTCATATTTTTGTGCAGAAGATGTGAGAGACAAAGTAAAACTCCACCAGCATACAAAGAAGCCATTGCTAATCAGAAAGCAGGTCACCCTAGTGGAGTTTGCAGATTATGTCAGAACCTGGAGCGCTTACCATCAGTGGAAGCAGGATCCAAAGAACAAAGATAAAGAAGATGTAGCAGATTGGTTTATTAAAGAGTCACTAAGGAGGAGGCCGGAACTTTCCACCAACACCAAAATTGAAGTTGTTTGGAATACTTTTTACAAACTTGGCAAAAGGGTCTGA","protein_sequence":"MSTFSASDFNSERYSSSRPSYPSDFYKMIDEYHDGERKLLVDVGCGPGTATLQMAQELKPFEQIIGSDLSATMIKTAEVIKEGSPDTYKNVSFKISSSDDFKFLGADSVDKQKIDMITAVECAHWFDFEKFQRSAYANLRKDGTIAIWGYADPIFPDYPEFDDLMIEVPYGKQGLGPYWEQPGRSRLRNMLKDSHLDPELFHDIQVSYFCAEDVRDKVKLHQHTKKPLLIRKQVTLVEFADYVRTWSAYHQWKQDPKNKDKEDVADWFIKESLRRRPELSTNTKIEVVWNTFYKLGKRV"}]}