{"ymdb_id":"YMDB00401","created_at":"2011-05-29T18:13:10.000Z","updated_at":"2016-09-08T18:35:27.000Z","name":"Porphobilinogen","cas":"487-90-1","state":"Solid","melting_point":null,"description":"Porphobilinogen is an intermediate in tetrapyrrole biosynthesis pathway. Uroporphyrinogen-III, the final product in this pathway, is a major branch point that leads to biosynthesis of different tetrapyrrole compounds (e.g. porphyrins). Tetrapyrroles usually function as a metal-binding cofactor in many important enzymes, proteins and pigments, such as heme, chlorophyll, cobalamine, siroheme, and cofator F430. [Biocyc PWY-5189]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Frydman, Benjamin; Despuy, Maria E.; Rapoport, Henry. Pyrroles from azaindoles. A synthesis of porphobilinogen. Journal of the American Chemical Society (1965), 87(15), 3530-1.","chebi_id":"17381","hmdb_id":"HMDB00245","kegg_id":"C00931","pubchem_id":"1021","cs_id":"995","foodb_id":null,"wikipedia_link":"Porphobilinogen","biocyc_id":"PORPHOBILINOGEN","iupac":"3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid","traditional_iupac":"porphobilinogen","logp":"-2.6797758986088773","pka":"4.3999884503565605","alogps_solubility":"2.72e+00 g/l","alogps_logp":"-2.40","alogps_logs":"-1.92","acceptor_count":"5","donor_count":"4","rotatable_bond_count":"6","polar_surface_area":"116.41","refractivity":"56.3839","polarizability":"22.557878019255046","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"8.782950994059014","pka_strongest_acidic":"3.6647253376201103","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["5-(aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionate","5-(aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionic acid","PBG","Porphobilinogen"],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"},{"name":"Porphyrin Metabolism","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":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."}],"proteins":[{"created_at":"2011-05-26T17:55:05.000Z","updated_at":"2011-05-27T15:01:02.000Z","name":"Delta-aminolevulinic acid dehydratase","uniprot_id":"P05373","uniprot_name":"HEM2_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM2","num_residues":342,"molecular_weight":"37739.69922","theoretical_pi":"6.05","general_function":"Involved in porphobilinogen synthase activity","specific_function":"Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen","reactions":[{"id":1905,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2495,"direction":"\u003e","locations":null,"altext":"2 5-aminolevulinate = porphobilinogen + 2 H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1OHL","cellular_location":null,"genbank_gene_id":"AY692744","genbank_protein_id":"51012939","gene_card_id":"HEM2","chromosome_location":"chromosome 7","locus":"YGL040C","synonyms":["ALADH","Porphobilinogen synthase"],"enzyme_classes":["4.2.1.24"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" porphobilinogen synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" cellular biosynthetic process"},{"category":"Process","description":" heterocycle biosynthetic process"},{"category":"Process","description":" tetrapyrrole biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"ALAD","identifier":"PF00490"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGCATACAGCTGAATTTTTGGAAACAGAACCAACAGAAATCTCATCTGTTCTAGCAGGTGGTTATAATCACCCACTGCTGAGACAGTGGCAAAGTGAGCGTCAACTGACTAAGAACATGTTGATTTTTCCGCTATTCATCTCCGATAATCCAGATGACTTTACTGAAATTGACTCTCTACCTAATATCAATAGAATCGGTGTAAATAGGCTAAAAGACTACTTAAAGCCATTAGTGGCCAAGGGTTTGCGTTCTGTGATCTTGTTTGGTGTGCCTCTCATCCCTGGTACCAAGGATCCAGTGGGTACAGCGGCTGACGATCCTGCAGGGCCAGTCATTCAAGGTATTAAATTCATTCGTGAGTATTTCCCTGAACTGTATATTATTTGCGATGTCTGTCTCTGTGAATACACTTCTCATGGCCATTGCGGGGTTCTATACGATGATGGTACTATTAATAGAGAACGTAGTGTCTCTAGATTAGCAGCTGTGGCAGTTAACTACGCTAAAGCTGGTGCGCACTGTGTGGCTCCCAGTGATATGATCGATGGTAGGATCAGAGATATTAAACGAGGCTTAATAAATGCAAACTTGGCTCACAAGACCTTCGTGTTATCCTATGCAGCTAAGTTTAGCGGTAATCTATATGGGCCATTCCGTGATGCTGCTTGTTCAGCTCCTTCGAATGGTGATAGGAAATGTTACCAATTACCTCCTGCCGGTCGTGGCCTGGCACGTAGGGCGTTGGAAAGGGATATGAGTGAAGGTGCCGACGGTATTATTGTTAAGCCTTCCACTTTCTACTTAGATATAATGAGGGATGCAAGTGAAATTTGTAAAGACTTACCAATCTGCGCATATCACGTGTCGGGCGAATACGCAATGTTACATGCTGCAGCTGAAAAAGGTGTTGTTGATTTGAAGACAATTGCCTTTGAATCTCATCAAGGTTTCTTGAGGGCGGGTGCCAGATTAATCATCACTTATTTGGCTCCTGAGTTCCTAGACTGGTTAGATGAAGAAAACTAA","protein_sequence":"MHTAEFLETEPTEISSVLAGGYNHPLLRQWQSERQLTKNMLIFPLFISDNPDDFTEIDSLPNINRIGVNRLKDYLKPLVAKGLRSVILFGVPLIPGTKDPVGTAADDPAGPVIQGIKFIREYFPELYIICDVCLCEYTSHGHCGVLYDDGTINRERSVSRLAAVAVNYAKAGAHCVAPSDMIDGRIRDIKRGLINANLAHKTFVLSYAAKFSGNLYGPFRDAACSAPSNGDRKCYQLPPAGRGLARRALERDMSEGADGIIVKPSTFYLDIMRDASEICKDLPICAYHVSGEYAMLHAAAEKGVVDLKTIAFESHQGFLRAGARLIITYLAPEFLDWLDEEN"},{"created_at":"2011-05-26T18:11:47.000Z","updated_at":"2011-05-27T15:01:03.000Z","name":"Porphobilinogen deaminase","uniprot_id":"P28789","uniprot_name":"HEM3_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM3","num_residues":327,"molecular_weight":"36674.19922","theoretical_pi":"6.32","general_function":"Involved in hydroxymethylbilane synthase activity","specific_function":"Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps","reactions":[{"id":1647,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2515,"direction":"\u003e","locations":null,"altext":"4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X99000","genbank_protein_id":"1429351","gene_card_id":"HEM3","chromosome_location":"chromosome 4","locus":"YDL205C","synonyms":["PBG","Hydroxymethylbilane synthase","HMBS","Pre-uroporphyrinogen synthase"],"enzyme_classes":["2.5.1.61"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring alkyl or aryl (other than methyl) groups"},{"category":"Function","description":" hydroxymethylbilane synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" macromolecule metabolic process"},{"category":"Process","description":" macromolecule modification"},{"category":"Process","description":" protein modification process"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" cellular biosynthetic process"},{"category":"Process","description":" heterocycle biosynthetic process"},{"category":"Process","description":" tetrapyrrole biosynthetic process"},{"category":"Process","description":" post-translational protein modification"},{"category":"Process","description":" protein-cofactor linkage"},{"category":"Process","description":" peptidyl-pyrromethane cofactor linkage"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Porphobil_deam","identifier":"PF01379"},{"name":"Porphobil_deamC","identifier":"PF03900"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGGGCCCTGAAACTCTACATATTGGTGGGAGAAAATCGAAATTGGCGGTAATACAATCCAACCATGTTTTAAAACTGATCGAAGAAAAGTATCCGGACTACGACTGCAAGGTTTTCACTTTGCAAACTCTTGGTGACCAGATTCAATTCAAACCTTTGTACTCATTTGGCGGTAAAGCTTTATGGACAAAGGAGTTGGAAGACCATCTTTACCATGACGATCCCTCAAAGAAGCTTGACTTGATCGTTCATTCTCTGAAGGACATGCCCACTTTACTACCAGAGGGTTTCGAGCTGGGGGGTATCACTAAGCGGGTCGATCCAACAGATTGTCTTGTCATGCCCTTTTACTCTGCTTATAAGTCTCTGGATGACCTTCCAGACGGGGGGATTGTGGGAACCTCATCCGTGAGAAGATCTGCTCAGCTAAAAAGAAAATACCCACATTTGAAATTTGAAAGTGTCAGAGGAAATATACAAACTAGATTACAAAAACTAGACGACCCAAAATCTCCGTACCAATGCATCATCTTGGCGTCTGCTGGGTTGATGCGTATGGGGTTGGAAAACAGAATTACGCAGCGATTCCATTCGGATACAATGTACCATGCAGTTGGACAAGGCGCCCTGGGTATAGAAATTAGAAAGGGTGACACCAAGATGATGAAGATTCTTGACGAAATTTGCGATCTAAATGCAACTATATGTTGCCTTTCGGAGCGTGCTTTGATGAGAACTTTAGAGGGGGGTTGTTCCGTTCCTATTGGTGTGGAATCTAAATACAATGAAGAGACTAAAAAATTACTATTAAAGGCCATTGTAGTTGACGTTGAAGGCACAGAAGCAGTAGAAGACGAAATTGAAATGCTAATAGAAAATGTTAAAGAAGATTCCATGGCGTGTGGTAAGATACTAGCTGAAAGAATGATTGCCGATGGCGCAAAGAAAATTCTGGATGAAATTAATTTAGACAGAATCAAATGA","protein_sequence":"MGPETLHIGGRKSKLAVIQSNHVLKLIEEKYPDYDCKVFTLQTLGDQIQFKPLYSFGGKALWTKELEDHLYHDDPSKKLDLIVHSLKDMPTLLPEGFELGGITKRVDPTDCLVMPFYSAYKSLDDLPDGGIVGTSSVRRSAQLKRKYPHLKFESVRGNIQTRLQKLDDPKSPYQCIILASAGLMRMGLENRITQRFHSDTMYHAVGQGALGIEIRKGDTKMMKILDEICDLNATICCLSERALMRTLEGGCSVPIGVESKYNEETKKLLLKAIVVDVEGTEAVEDEIEMLIENVKEDSMACGKILAERMIADGAKKILDEINLDRIK"}]}