{"ymdb_id":"YMDB00084","created_at":"2011-05-29T15:55:08.000Z","updated_at":"2016-09-08T18:34:59.000Z","name":"Coproporphyrinogen III","cas":"2624-63-7","state":"Solid","melting_point":null,"description":"Coproporphyrinogen III is an intermediate in the heme biosynthesis from uroporphyrinogen-III pathway. Coproporphyrinogen III is obtained from uroporphyrinogen III by the enzyme uroporphyrinogen III decarboxylase and converted to protoporphyrinogen IX; uroporphyrinogen-III is a major branch point that leads to biosynthesis of different tetrapyrrole compounds (e.g. porphyrins). Protoheme IX is the final product in this pathway but different derivatives of protoheme can actually be formed that differ in modifications to the porphyrin ring, including how it is bound to the protein (e.g. heme o, heme a, heme c, and heme d). [Biocyc HEME-BIOSYNTHESIS-II]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":"Shoolingin-Jordan, Peter M.  The biosynthesis of coproporphyrinogen III.    Porphyrin Handbook  (2003),  12  33-74.","chebi_id":"15439","hmdb_id":"HMDB01261","kegg_id":"C03263","pubchem_id":"321","cs_id":"315","foodb_id":null,"wikipedia_link":"Coproporphyrinogen_III","biocyc_id":"COPROPORPHYRINOGEN_III","iupac":"3-[9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid","traditional_iupac":"3-[9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid","logp":"4.891239218666666","pka":"4.229360781234833","alogps_solubility":"1.12e-02 g/l","alogps_logp":"1.96","alogps_logs":"-4.77","acceptor_count":"8","donor_count":"8","rotatable_bond_count":"12","polar_surface_area":"212.35999999999996","refractivity":"181.86080000000013","polarizability":"72.85338000201646","formal_charge":"0","physiological_charge":"-4","pka_strongest_basic":null,"pka_strongest_acidic":"3.8015317067975603","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-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropanoate","3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropanoic acid","5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-2,7,12,18-Porphinetetrapropionate","5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-2,7,12,18-Porphinetetrapropionic acid","5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21H,23H-Porphine-2,7,12,18-tetrapropanoate","5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21H,23H-Porphine-2,7,12,18-tetrapropanoic acid","coproporphyrinogen","coproporphyrinogen III","coproporphyrinogen-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":"2011-05-26T17:55:45.000Z","updated_at":"2011-07-22T17:54:31.000Z","name":"Coproporphyrinogen-III oxidase","uniprot_id":"P11353","uniprot_name":"HEM6_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM13","num_residues":328,"molecular_weight":"37711.30078","theoretical_pi":"6.8","general_function":"Involved in coproporphyrinogen oxidase activity","specific_function":"Key enzyme in heme biosynthesis. Catalyzes the oxidative decarboxylation of propionic acid side chains of rings A and B of coproporphyrinogen III","reactions":[{"id":1414,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2496,"direction":"\u003e","locations":"Cytoplasm","altext":"Coproporphyrinogen-III + O(2) + 2 H(+) = protoporphyrinogen-IX + 2 CO(2) + 2 H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1TLB","cellular_location":"Cytoplasm","genbank_gene_id":"AY557656","genbank_protein_id":"45269205","gene_card_id":"HEM13","chromosome_location":"chromosome 4","locus":"YDR044W","synonyms":["COX","Coprogen oxidase","Coproporphyrinogenase"],"enzyme_classes":["1.3.3.3"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" coproporphyrinogen oxidase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-CH group of donors"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"},{"category":"Process","description":" porphyrin biosynthetic process"}],"pfams":[{"name":"Coprogen_oxidas","identifier":"PF01218"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGCCTGCCCCTCAAGATCCAAGGAATCTTCCAATTAGACAACAAATGGAAGCCCTTATCCGTCGCAAACAAGCTGAAATCACGCAAGGTTTGGAATCCATCGATACTGTTAAGTTCCACGCTGATACTTGGACCCGTGGTAACGATGGTGGTGGTGGTACCTCTATGGTTATCCAAGACGGTACAACTTTCGAAAAAGGTGGTGTTAATGTCTCCGTTGTTTATGGTCAATTGAGCCCAGCGGCCGTTTCAGCCATGAAAGCTGATCATAAGAATCTGCGTCTACCAGAAGATCCAAAGACTGGTTTGCCAGTTACCGACGGTGTCAAGTTCTTCGCTTGTGGTTTAAGTATGGTCATTCATCCCGTTAACCCACACGCTCCAACCACGCACTTAAACTACCGTTACTTCGAAACTTGGAACCAAGATGGGACCCCACAAACTTGGTGGTTTGGTGGTGGTGCTGATTTGACACCTTCTTACTTATACGAAGAAGACGGTCAATTATTCCACCAACTGCACAAGGATGCCTTGGACAAGCACGACACTGCTTTGTACCCACGTTTCAAGAAATGGTGTGATGAGTACTTCTACATTACCCACCGTAAGGAAACACGTGGTATTGGTGGTATATTCTTTGACGATTATGATGAACGTGACCCACAAGAAATATTGAAGATGGTTGAAGACTGTTTCGATGCTTTCTTGCCATCCTACTTGACTATCGTCAAGAGAAGAAAAGATATGCCATATACAAAGGAAGAACAACAATGGCAGGCCATTAGACGTGGTAGATACGTTGAATTCAACTTAATCTACGATAGAGGTACCCAATTCGGTTTGAGAACCCCAGGCTCTAGAGTTGAGTCAATTTTGATGAGTTTGCCTGAACATGCTTCATGGTTATACAACCACCACCCTGCTCCTGGTTCCAGAGAAGCTAAATTACTAGAAGTTACCACCAAACCAAGAGAGTGGGTTAAATAA","protein_sequence":"MPAPQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK"},{"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"}]}