{"ymdb_id":"YMDB00267","created_at":"2011-05-29T18:00:23.000Z","updated_at":"2016-09-08T18:35:16.000Z","name":"Uroporphyrinogen III","cas":"1976-85-8","state":"Solid","melting_point":null,"description":"Uroporphyrinogen-III is the final product in tetrapyrrole biosynthesis pathway which starts with the formation of 5-aminolevulinic acid from glycine and succinyl CoA by the enzyme ALA synthase. Uroporphyrinogen-III 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":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"15437","hmdb_id":"HMDB01086","kegg_id":"C01051","pubchem_id":"1179","cs_id":"1146","foodb_id":null,"wikipedia_link":"Uroporphyrinogen_III","biocyc_id":"UROPORPHYRINOGEN-III","iupac":"3-[9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetrakis(carboxymethyl)-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid","traditional_iupac":"uroporphyrinogen-III","logp":"1.3885468186666658","pka":"3.5861502444706224","alogps_solubility":"4.37e-02 g/l","alogps_logp":"0.67","alogps_logs":"-4.28","acceptor_count":"16","donor_count":"12","rotatable_bond_count":"20","polar_surface_area":"361.55999999999995","refractivity":"206.9264000000002","polarizability":"81.5514750357378","formal_charge":"0","physiological_charge":"-8","pka_strongest_basic":null,"pka_strongest_acidic":"3.2116775904243284","bioavailability":"0","number_of_rings":"5","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-2,7,12,18-Porphinetetrapropionate","3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-2,7,12,18-Porphinetetrapropionic acid","3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-21H,23H-Porphine-2,7,12,18-tetrapropanoate","3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-21H,23H-Porphine-2,7,12,18-tetrapropanoic acid","3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropanoate","3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropanoic acid","Urogen III","Uroporphyrinogen III","uroporphyrinogen-III"],"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."},{"pubmed_id":8234090,"citation":"Chelstowska, A., Rytka, J. (1993). \"[Biosynthesis of heme in yeast Saccharomyces cerevisiae].\" Postepy Biochem 39:173-185."},{"pubmed_id":14559249,"citation":"Hoffman, M., Gora, M., Rytka, J. (2003). \"Identification of rate-limiting steps in yeast heme biosynthesis.\" Biochem Biophys Res Commun 310:1247-1253."}],"proteins":[{"created_at":"2011-05-24T20:23:06.000Z","updated_at":"2011-05-27T14:56:00.000Z","name":"Uroporphyrinogen-III C-methyltransferase","uniprot_id":"P36150","uniprot_name":"SUMT_YEAST","enzyme":true,"transporter":false,"gene_name":"MET1","num_residues":593,"molecular_weight":"66124.70313","theoretical_pi":"6.53","general_function":"Involved in methyltransferase activity","specific_function":"Siroheme synthase involved in methionine biosynthesis","reactions":[{"id":2041,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2312,"direction":"\u003e","locations":null,"altext":"S-adenosyl-L-methionine + uroporphyrinogen III = S-adenosyl-L-homocysteine + precorrin-1.","export":false,"pw_reaction_id":null,"source":null},{"id":2313,"direction":"\u003e","locations":null,"altext":"S-adenosyl-L-methionine + precorrin-1 = S-adenosyl-L-homocysteine + precorrin-2.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"Z28294","genbank_protein_id":"486539","gene_card_id":"MET1","chromosome_location":"chromosome 11","locus":"YKR069W","synonyms":["Urogen III methylase","SUMT","Uroporphyrinogen III methylase","UROM"],"enzyme_classes":["2.1.1.107"],"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":"Function","description":" C-methyltransferase activity"},{"category":"Function","description":" uroporphyrin-III C-methyltransferase activity"},{"category":"Process","description":" porphyrin biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" heme biosynthetic process"},{"category":"Process","description":" siroheme biosynthetic process"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"}],"pfams":[{"name":"TP_methylase","identifier":"PF00590"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGGTACGAGACTTAGTGACATTGCCTTCATCACTGCCCTTGATTACTGCTGGTTTTGCTACTGATCAGGTTCATTTGCTTATTGGTACAGGGTCCACGGACTCAGTAAGCGTTTGTAAGAATAGAATCCACTCCATTTTGAATGCTGGTGGTAATCCCATAGTAGTGAATCCCTCGTCACCAAGCCATACTAAACAATTACAATTGGAATTTGGTAAGTTTGCAAAGTTCGAAATAGTAGAAAGGGAGTTTAGGTTATCTGATTTAACTACTTTGGGGAGAGTTCTGGTATGCAAGGTAGTGGATAGAGTATTCGTAGATCTACCCATAACACAAAGTCGCCTATGCGAGGAGATCTTTTGGCAATGCCAAAAACTGAGAATTCCCATAAATACATTCCACAAACCAGAGTTTTCTACCTTCAATATGATTCCTACGTGGGTCGACCCAAAAGGAAGTGGTTTACAAATCTCAGTTACTACGAATGGGAATGGATACATCTTGGCAAACAGGATAAAAAGAGATATAATATCACACTTACCTCCAAACATATCTGAGGTGGTGATAAACATGGGGTATTTGAAAGACCGTATTATAAACGAAGACCATAAGGCCTTGTTAGAGGAAAAGTACTACCAGACTGACATGTCATTACCTGGATTTGGCTACGGCTTAGATGAGGACGGTTGGGAGAGCCATAAGTTTAATAAGCTAATTCGTGAATTTGAAATGACCAGTAGAGAACAGAGACTTAAGAGAACCAGATGGTTATCTCAGATAATGGAGTATTACCCGATGAACAAGCTGAGTGACATCAAGTTGGAAGATTTCGAGACTTCATCTTCTCCAAATAAAAAGACAAAGCAGGAAACTGTCACAGAGGGTGTAGTACCTCCTACCGATGAAAATATTGAAAACGGTACAAAACAACTACAATTATCGGAAGTGAAAAAAGAGGAGGGACCTAAAAAACTAGGGAAGATTTCTTTAGTCGGAAGTGGTCCAGGCTCGGTATCTATGCTAACGATAGGTGCATTACAAGAAATAAAGTCTGCAGATATAATACTGGCAGATAAACTGGTACCGCAAGCCATTTTAGATTTAATACCTCCAAAAACTGAAACCTTCATAGCCAAAAAATTTCCCGGTAATGCAGAACGAGCACAACAGGAATTACTAGCTAAAGGTTTAGAATCGTTGGATAATGGATTGAAAGTAGTCCGTTTGAAGCAAGGTGATCCGTATATTTTTGGCCGTGGTGGCGAGGAATTTAATTTCTTCAAAGATCACGGATATATTCCTGTGGTTTTACCGGGCATAAGCTCATCCCTAGCTTGTACTGTATTGGCTCAGATACCCGCTACTCAACGTGATATAGCAGACCAAGTGCTCATATGTACTGGGACTGGGAGAAAGGGCGCTCTGCCTATAATTCCTGAATTTGTTGAAAGCAGAACCACCGTCTTTCTAATGGCACTGCATCGCGCCAACGTTCTGATCACGGGATTATTGAAGCATGGCTGGGATGGTGATGTCCCCGCTGCAATTGTCGAGAGAGGATCGTGCCCTGACCAGCGTGTTACTAGAACTCTTCTTAAATGGGTACCAGAAGTCGTGGAGGAGATTGGTTCAAGGCCCCCCGGTGTCTTGGTTGTAGGCAAGGCTGTGAATGCATTGGTTGAAAAAGATCTGATAAATTTTGACGAATCAAGAAAATTTGTCATTGATGAAGGTTTTAGAGAATTTGAGGTTGATGTAGATAGTCTATTTAAGTTATACTAA","protein_sequence":"MVRDLVTLPSSLPLITAGFATDQVHLLIGTGSTDSVSVCKNRIHSILNAGGNPIVVNPSSPSHTKQLQLEFGKFAKFEIVEREFRLSDLTTLGRVLVCKVVDRVFVDLPITQSRLCEEIFWQCQKLRIPINTFHKPEFSTFNMIPTWVDPKGSGLQISVTTNGNGYILANRIKRDIISHLPPNISEVVINMGYLKDRIINEDHKALLEEKYYQTDMSLPGFGYGLDEDGWESHKFNKLIREFEMTSREQRLKRTRWLSQIMEYYPMNKLSDIKLEDFETSSSPNKKTKQETVTEGVVPPTDENIENGTKQLQLSEVKKEEGPKKLGKISLVGSGPGSVSMLTIGALQEIKSADIILADKLVPQAILDLIPPKTETFIAKKFPGNAERAQQELLAKGLESLDNGLKVVRLKQGDPYIFGRGGEEFNFFKDHGYIPVVLPGISSSLACTVLAQIPATQRDIADQVLICTGTGRKGALPIIPEFVESRTTVFLMALHRANVLITGLLKHGWDGDVPAAIVERGSCPDQRVTRTLLKWVPEVVEEIGSRPPGVLVVGKAVNALVEKDLINFDESRKFVIDEGFREFEVDVDSLFKLY"},{"created_at":"2011-05-26T17:56:13.000Z","updated_at":"2011-05-27T15:01:03.000Z","name":"Uroporphyrinogen decarboxylase","uniprot_id":"P32347","uniprot_name":"DCUP_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM12","num_residues":362,"molecular_weight":"41348.69922","theoretical_pi":"7.09","general_function":"Involved in uroporphyrinogen decarboxylase activity","specific_function":"Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III","reactions":[{"id":2040,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2497,"direction":"\u003e","locations":"Nucleus. Cytoplasm","altext":"Uroporphyrinogen III = coproporphyrinogen + 4 CO(2).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Nucleus. Cytoplasm","genbank_gene_id":"X63721","genbank_protein_id":"3767","gene_card_id":"HEM12","chromosome_location":"chromosome 4","locus":"YDR047W","synonyms":["UPD","URO-D"],"enzyme_classes":["4.1.1.37"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-carbon lyase activity"},{"category":"Function","description":" carboxy-lyase activity"},{"category":"Function","description":" uroporphyrinogen decarboxylase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"},{"category":"Process","description":" porphyrin biosynthetic process"}],"pfams":[{"name":"URO-D","identifier":"PF01208"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGGGTAACTTTCCAGCTCCAAAAAACGATTTGATATTGAGAGCCGCAAAGGGTGAAAAAGTCGAGAGACCGCCATGCTGGATAATGCGCCAGGCAGGTCGTTACCTGCCGGAATATCACGAGGTGAAAAACAATCGTGATTTCTTTCAAACTTGCAGGGATGCGGAAATTGCTTCTGAGATTACTATCCAGCCGGTAAGACGCTATAGAGGCCTCATTGATGCTGCTATTATTTTTAGTGATATCTTAGTTATTCCGCAAGCCATGGGTATGAGGGTCGAGATGCTCGAAGGTAAAGGTCCACATTTCCCAGAACCTTTAAGAAATCCGGAAGACCTCCAAACGGTATTAGACTACAAGGTTGATGTTTTGAAAGAGTTAGATTGGGCTTTCAAGGCAATCACCATGACAAGGATCAAGTTGGATGGTGAGGTTCCCTTATTTGGCTTTTGCGGGGGACCTTGGACTCTAATGGTTTATATGACGGAAGGCGGTGGATCCCGTCTTTTCAGATTTGCCAAACAATGGATTAACATGTATCCAGAGCTTTCTCACAAATTATTACAAAAAATCACTGATGTGGCCGTGGAGTTTCTGAGTCAGCAAGTCGTGGCGGGTGCTCAAATACTACAAGTTTTTGAAAGTTGGGGTGGTGAGCTTTCGTCTGTAGATTTTGATGAGTTTTCCCTACCATATTTAAGACAAATTGCCGAAAGAGTGCCTAAAAGATTGCAAGAATTAGGTATCATGGAACAGATTCCTATGATCGTTTTTGCGAAAGGGTCGTGGTATGCTTTGGACAAGCTATGCTGTTCAGGATTTGACGTTGTTTCGTTGGACTGGTCCTGGGACCCAAGAGAAGCGGTAAAAATAAACAAGAACCGTGTCACCTTGCAGGGCAACCTGGATCCTGGCGTCATGTATGGTTCTAAAGAGGTAATAACAAAGAAAGTTAAACAGATGATTGAGGCTTTTGGAGGTGGGAAGTCCCGCTACATTGTTAATTTCGGTCACGGTACCCACCCTTTCATGGATCCAGACGTCATCAAGTTTTTCTTGGAGGAGTGCCACAGAATTGGTTCGAAGTAA","protein_sequence":"MGNFPAPKNDLILRAAKGEKVERPPCWIMRQAGRYLPEYHEVKNNRDFFQTCRDAEIASEITIQPVRRYRGLIDAAIIFSDILVIPQAMGMRVEMLEGKGPHFPEPLRNPEDLQTVLDYKVDVLKELDWAFKAITMTRIKLDGEVPLFGFCGGPWTLMVYMTEGGGSRLFRFAKQWINMYPELSHKLLQKITDVAVEFLSQQVVAGAQILQVFESWGGELSSVDFDEFSLPYLRQIAERVPKRLQELGIMEQIPMIVFAKGSWYALDKLCCSGFDVVSLDWSWDPREAVKINKNRVTLQGNLDPGVMYGSKEVITKKVKQMIEAFGGGKSRYIVNFGHGTHPFMDPDVIKFFLEECHRIGSK"},{"created_at":"2011-05-27T02:40:51.000Z","updated_at":"2011-05-27T15:01:18.000Z","name":"Uroporphyrinogen-III synthase","uniprot_id":"P06174","uniprot_name":"HEM4_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM4","num_residues":275,"molecular_weight":"30911.30078","theoretical_pi":"8.44","general_function":"Involved in uroporphyrinogen-III synthase activity","specific_function":"Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III","reactions":[{"id":2042,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2685,"direction":"\u003e","locations":null,"altext":"Hydroxymethylbilane = uroporphyrinogen III + H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X89633","genbank_protein_id":"1279703","gene_card_id":"HEM4","chromosome_location":"chromosome 15","locus":"YOR278W","synonyms":["UROIIIS","UROS","Hydroxymethylbilane hydrolyase [cyclizing]","Uroporphyrinogen-III cosynthase"],"enzyme_classes":["4.2.1.75"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" uroporphyrinogen-III synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" cellular biosynthetic process"},{"category":"Process","description":" heterocycle biosynthetic process"},{"category":"Process","description":" tetrapyrrole biosynthetic process"}],"pfams":[{"name":"HEM4","identifier":"PF02602"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGTCTAGTCGTAAAAAAGTCAGAGTATTACTGCTCAAGAATAAAACTGTCCCCATTGATAAATATGAATTGGAGTGTAGGAGTAAGGCGTTTGAACCCATATTCGTACCGCTTATTAAACATACACATGTAATTCAAGATTTTAGAAATGTTTTGAATACCATCCCAAACTATTTGAATACTATCAATTACATTATTATTACCTCTCAAAGGACTGTAGAGTCATTGAATGAAGCGATCATTCCCACATTGACAAGTGAACAAAAAGCTGCATTGCTCAGTAAAACAGTTTATACTGTAGGCCCTGCTACTGCTAACTTCATCAGAAGATCAGGTTTCATTAATGTTAAAGGTGGAGAAGACGCTGGTAATGGTTCAATCCTTGCTGATATAATTATTGATGACTTGAGTACGGATATTAAGGCATGCCCACCAAGTGAACTATTATTTCTCGTGGGTGAAATTAGAAGAGATATCATCCCAAAGAAACTCCATAGCAAGGGAATAAAAGTAAGAGAAGTGGTTACTTATAAAACTGAAGAATTAAGCGACGGTTTTAAAAGATTCATACACGCCATGAAAGAATGCGATGAGGATGAAGTATTCTCGGACTGGGTGGTAGTTTTCAGTCCCCAGGGAACGAAAGAAATTACTCAGTATTTGGGTGACAGTAACCGCCTACCAGGTTCCCATCTACGGGTTGCGTCCATCGGACCTACCACTAAAAAATATCTGGATGATAATGATGTAACCTCTGATGTGGTCAGTCCAAAACCGGACCCCAAGTCGCTATTAGATGCTATTGAATTATACCAGCGCCATAAATAA","protein_sequence":"MSSRKKVRVLLLKNKTVPIDKYELECRSKAFEPIFVPLIKHTHVIQDFRNVLNTIPNYLNTINYIIITSQRTVESLNEAIIPTLTSEQKAALLSKTVYTVGPATANFIRRSGFINVKGGEDAGNGSILADIIIDDLSTDIKACPPSELLFLVGEIRRDIIPKKLHSKGIKVREVVTYKTEELSDGFKRFIHAMKECDEDEVFSDWVVVFSPQGTKEITQYLGDSNRLPGSHLRVASIGPTTKKYLDDNDVTSDVVSPKPDPKSLLDAIELYQRHK"}]}