{"ymdb_id":"YMDB00156","created_at":"2011-05-29T16:02:15.000Z","updated_at":"2016-09-08T18:35:06.000Z","name":"Protoporphyrinogen IX","cas":"7412-77-3","state":"Solid","melting_point":null,"description":"Protoporphyrinogen IX is an intermediate in the heme biosynthesis from uroporphyrinogen-III pathway. In this pathway, protoporphyrinogen IX is obtained from coproporphyrinogen III and converted to protoporphyrin IX. 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":"","location":"mitochondrion;cytoplasm","synthesis_reference":null,"chebi_id":"15435","hmdb_id":"HMDB01097","kegg_id":"C01079","pubchem_id":"121893","cs_id":"108741","foodb_id":null,"wikipedia_link":"Protoporphyrinogen_IX","biocyc_id":"PROTOPORPHYRINOGEN","iupac":"3-[20-(2-carboxyethyl)-9,14-diethenyl-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-[20-(2-carboxyethyl)-9,14-diethenyl-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":"6.200009445999999","pka":"4.67011788729448","alogps_solubility":"5.51e-03 g/l","alogps_logp":"3.44","alogps_logs":"-5.01","acceptor_count":"4","donor_count":"6","rotatable_bond_count":"8","polar_surface_area":"137.76","refractivity":"169.41620000000003","polarizability":"64.5199264797442","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":null,"pka_strongest_acidic":"4.0668900795671075","bioavailability":"0","number_of_rings":"5","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["7,12-diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoate","7,12-diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoic acid","7,12-diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21h,23h-porphine-2,18-dipropanoate","7,12-diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21h,23h-porphine-2,18-dipropanoic acid","Protoporphyrinogen","protoporphyrinogen IX","protoporphyrinogen-IX"],"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":"2011-05-26T17:41:21.000Z","updated_at":"2011-05-27T15:01:02.000Z","name":"Protoporphyrinogen oxidase","uniprot_id":"P40012","uniprot_name":"PPOX_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM14","num_residues":539,"molecular_weight":"59702.39844","theoretical_pi":"9.8","general_function":"Involved in oxygen-dependent protoporphyrinogen oxidase activity","specific_function":"Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX","reactions":[{"id":1913,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2479,"direction":"\u003e","locations":"Mitochondrion inner membrane.","altext":"Protoporphyrinogen-IX + 3 O(2) = protoporphyrin-IX + 3 H(2)O(2).","export":false,"pw_reaction_id":null,"source":null},{"id":14203,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006644","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion inner membrane.","genbank_gene_id":"U18778","genbank_protein_id":"603606","gene_card_id":"HEM14","chromosome_location":"chromosome 5","locus":"YER014W","synonyms":["PPO"],"enzyme_classes":["1.3.3.4"],"go_classes":[{"category":"Component","description":" Not Available"},{"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":"Function","description":" oxygen-dependent protoporphyrinogen oxidase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"},{"category":"Process","description":" porphyrin biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"}],"pfams":[],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"},{"name":"Porphyrin Metabolism","kegg_map_id":null}],"gene_sequence":"ATGTTATTACCATTAACAAAGCTAAAACCGAGAGCAAAAGTTGCTGTTGTAGGGGGTGGCGTTTCTGGACTATGTTTTACTTATTTTTTAAGCAAGTTGAGACCGGATGTTGAAATCACACTGTTCGAATCGCAGAACAGAACTGGGGGTTGGATATATTCTTGTAACACAAGAGATATGAGTGGGAACCCAATTATGTTGGAGAAGGGACCCAGAACATTGAGGGGCGTATCAGACGGGACCGTTCTGATTATGGATACCCTTAAAGACTTGGGCAAGGAAGCAGTTATTCAAAGCATTGATAAAGGTTGCATTGCAGACAAAAAGTTTCTACTAGACCCCAGTGATAAACTCGTGCAGGTTCCTAATTCGATATCTACAACAGTAAAATTTCTGCTGAATCCGTTGGGAAAAGGACTCATCACGGGTATGATGGGAGAATGGTTCAGAAAAAAATCTCCACATCCTGGCCAAGACGAAAGTGTCGAATCCATTTGTGACAGAAGGTTTGGGAATAACTACATATCAAACAATATGATCAGTGCCTTACTAAGAGGTATCTATGGGGATGACGTTTCCCTATTAAGTGCCAAGAGAACGTTTAAGAAAATATACTACAATGAACTAAAGCACGGATCTAACACACAAGCTATGATTGATAATATGCGCGGAAAGTCAAGAAGTAAAAAAACTGAGAACCTGCACCAATCTTTAACTGGCTGCCTTAACGACTACTCAAATGCGTTTGGAAAAGACAGGTCAAAGTTATTAGACTTATCCAACACGCTAAAGAAATATCCCATGTTGGGTCTTGCTGGGGGACTAGAAACGTTTCCCAAGATAGTCAGAAATGCTTTGAACGAATTTAAAAACGTCAAAATAGTTACTGGGAACCCGGTTACGCAAATAATGAAACGCCCTGCTAACGAAACGACAATCGGATTGAAAGCGAAATCTGGCGACCAATACGAAACATTTGACCATTTAAGACTTACGATAACACCTCCCAAAATCGCTAAATTGCTACCGAAGGATCAAAATTCATTATCCAAGTTATTAGATGAGATACAATCAAACACAATAATTTTAGTTAATTATTATTTGCCAAACAAAGATGTAATAGATGCCGATCTACAAGGCTTTGGATACTTGGTTCCCAAATCCAATAAGAATCCAGGGAAATTGCTTGGTGTAATTTTCGATTCTGTTATCGAAAGGAATTTCAAACCACTTTTTGACAAACTCTCCACAAACCCAAACGCCCTCAACAAATATACAAAAGTGACTGCGATGATAGGAGGTTGTATGCTCAATGAACACGGTGTTCCTGTAGTGCCATCCAGGGAGGTAACCATTAATGCAGTCAAAGATGCGCTGAACAACCACCTCGGCATCAGTAACAAGGATCTGGAAGCTGGTCAGTGGGAATTCACTATCGCCGATAGATGTCTGCCAAGATTTCATGTAGGTTATGACGCATGGCAAGAAAGAGCTGAAAGGAAGTTGCAAGAATCTTACGGCCAAACAGTTTCTGTGGGGGGAATGGGATTTTCTAGAAGTCCCGGTGTCCCTGACGTTATTGTAGACGGCTTTAACGACGCCTTACAGCTAAGCAAATAA","protein_sequence":"MLLPLTKLKPRAKVAVVGGGVSGLCFTYFLSKLRPDVEITLFESQNRTGGWIYSCNTRDMSGNPIMLEKGPRTLRGVSDGTVLIMDTLKDLGKEAVIQSIDKGCIADKKFLLDPSDKLVQVPNSISTTVKFLLNPLGKGLITGMMGEWFRKKSPHPGQDESVESICDRRFGNNYISNNMISALLRGIYGDDVSLLSAKRTFKKIYYNELKHGSNTQAMIDNMRGKSRSKKTENLHQSLTGCLNDYSNAFGKDRSKLLDLSNTLKKYPMLGLAGGLETFPKIVRNALNEFKNVKIVTGNPVTQIMKRPANETTIGLKAKSGDQYETFDHLRLTITPPKIAKLLPKDQNSLSKLLDEIQSNTIILVNYYLPNKDVIDADLQGFGYLVPKSNKNPGKLLGVIFDSVIERNFKPLFDKLSTNPNALNKYTKVTAMIGGCMLNEHGVPVVPSREVTINAVKDALNNHLGISNKDLEAGQWEFTIADRCLPRFHVGYDAWQERAERKLQESYGQTVSVGGMGFSRSPGVPDVIVDGFNDALQLSK"},{"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":" 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":"Function","description":" coproporphyrinogen oxidase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"},{"category":"Process","description":" porphyrin biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"}],"pfams":[{"name":"Coprogen_oxidas","identifier":"PF01218"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGCCTGCCCCTCAAGATCCAAGGAATCTTCCAATTAGACAACAAATGGAAGCCCTTATCCGTCGCAAACAAGCTGAAATCACGCAAGGTTTGGAATCCATCGATACTGTTAAGTTCCACGCTGATACTTGGACCCGTGGTAACGATGGTGGTGGTGGTACCTCTATGGTTATCCAAGACGGTACAACTTTCGAAAAAGGTGGTGTTAATGTCTCCGTTGTTTATGGTCAATTGAGCCCAGCGGCCGTTTCAGCCATGAAAGCTGATCATAAGAATCTGCGTCTACCAGAAGATCCAAAGACTGGTTTGCCAGTTACCGACGGTGTCAAGTTCTTCGCTTGTGGTTTAAGTATGGTCATTCATCCCGTTAACCCACACGCTCCAACCACGCACTTAAACTACCGTTACTTCGAAACTTGGAACCAAGATGGGACCCCACAAACTTGGTGGTTTGGTGGTGGTGCTGATTTGACACCTTCTTACTTATACGAAGAAGACGGTCAATTATTCCACCAACTGCACAAGGATGCCTTGGACAAGCACGACACTGCTTTGTACCCACGTTTCAAGAAATGGTGTGATGAGTACTTCTACATTACCCACCGTAAGGAAACACGTGGTATTGGTGGTATATTCTTTGACGATTATGATGAACGTGACCCACAAGAAATATTGAAGATGGTTGAAGACTGTTTCGATGCTTTCTTGCCATCCTACTTGACTATCGTCAAGAGAAGAAAAGATATGCCATATACAAAGGAAGAACAACAATGGCAGGCCATTAGACGTGGTAGATACGTTGAATTCAACTTAATCTACGATAGAGGTACCCAATTCGGTTTGAGAACCCCAGGCTCTAGAGTTGAGTCAATTTTGATGAGTTTGCCTGAACATGCTTCATGGTTATACAACCACCACCCTGCTCCTGGTTCCAGAGAAGCTAAATTACTAGAAGTTACCACCAAACCAAGAGAGTGGGTTAAATAA","protein_sequence":"MPAPQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK"}]}