{"ymdb_id":"YMDB00055","created_at":"2011-05-29T15:52:27.000Z","updated_at":"2016-09-08T18:34:57.000Z","name":"Protoporphyrin IX","cas":"553-12-8","state":"Solid","melting_point":"300 oC","description":"Protoporphyrin IX is an intermediate in the heme biosynthesis from uroporphyrinogen-III pathway. In this pathway, protoporphyrin IX is obtained from protoporphyrinogen IX and converted to protoheme 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":"0.169 mg/mL at 25 oC [YALKOWSKY,SH \u0026 DANNENFELSER,RM (1992)]","experimental_logp_hydrophobicity":"","location":"mitochondrion","synthesis_reference":"Games, David E.; Jackson, Anthony H.; Jackson, J. Richard; Belcher, Roderick V.; Smith, Sydney G.  Biosynthesis of protoporphyrin-IX from coproporphyrinogen-III.    Journal of the Chemical Society, Chemical Communications  (1976),   (6),  187-8. ","chebi_id":"15430","hmdb_id":"HMDB00241","kegg_id":"C02191","pubchem_id":"4971","cs_id":"10469486","foodb_id":null,"wikipedia_link":"Protoporphyrin_IX","biocyc_id":"PROTOPORPHYRIN_IX","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(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-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(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-4-yl]propanoic acid","logp":"6.778796967715938","pka":"4.128117407779678","alogps_solubility":"2.17e-02 g/l","alogps_logp":"4.40","alogps_logs":"-4.41","acceptor_count":"6","donor_count":"4","rotatable_bond_count":"8","polar_surface_area":"131.96","refractivity":"163.81120000000004","polarizability":"66.03349029270831","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"4.958835229373015","pka_strongest_acidic":"3.684359896427431","bioavailability":"0","number_of_rings":"5","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["3,3'-(3,7,12,17-tetramethyl-8,13-divinyl-21H,23H-porphine-2,18-diyl)-bis-propionate","3,3'-(3,7,12,17-tetramethyl-8,13-divinyl-21H,23H-porphine-2,18-diyl)-bis-propionic acid","3,3'-(3,7,12,17-tetramethyl-8,13-divinylporphine-2,18-diyl)di","3,7,12,17-Tetramethyl-8,13-divinylporphyrin-2,18-dipropanoate","3,7,12,17-Tetramethyl-8,13-divinylporphyrin-2,18-dipropanoic acid","H2PpIX","Kammerer's prophyrin","Ooporphyrin","Porphyrinogen IX","ppIX","Protoporphyrin","Protoporphyrin IX","Protoporphyrin-\"ix\"","protoporphyrin-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":12397956,"citation":"Strakhovskaia, M. G., Shumarina, A. O., Fraikin, G. I. a., Rubin, A. B. (2002). \"[Fluorescent photobleaching of endogenous protoporphyrin IX in yeast cells].\" Biofizika 47:852-857."},{"pubmed_id":10365443,"citation":"Strakhovskaya, M. G., Shumarina, A. O., Fraikin, G. Y. a., Rubin, A. B. (1999). \"Endogenous porphyrin accumulation and photosensitization in the yeast Saccharomyces cerevisiae in the presence of 2,2'-dipyridyl.\" J Photochem Photobiol B 49:18-22."},{"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":"2011-05-24T21:11:28.000Z","updated_at":"2011-07-22T17:55:05.000Z","name":"Ferrochelatase, mitochondrial","uniprot_id":"P16622","uniprot_name":"HEMH_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM15","num_residues":393,"molecular_weight":"44595.80078","theoretical_pi":"9.46","general_function":"Involved in ferrochelatase activity","specific_function":"Catalyzes the ferrous insertion into protoporphyrin IX","reactions":[{"id":1538,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2366,"direction":"\u003e","locations":"Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.","altext":"Protoheme + 2 H(+) = protoporphyrin + Fe(2+).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1LBQ","cellular_location":"Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.","genbank_gene_id":"J05395","genbank_protein_id":"171660","gene_card_id":"HEM15","chromosome_location":"chromosome 15","locus":"YOR176W","synonyms":["Heme synthase","Protoheme ferro-lyase"],"enzyme_classes":["4.99.1.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" ferrochelatase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" heme biosynthetic process"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"},{"category":"Process","description":" porphyrin biosynthetic process"}],"pfams":[{"name":"Ferrochelatase","identifier":"PF00762"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGCTTTCCAGAACAATCCGTACACAAGGTTCCTTCCTAAGAAGATCACAACTGACCATTACAAGATCATTTTCGGTTACATTCAACATGCAGAATGCACAAAAGAGATCACCCACAGGAATTGTTTTGATGAACATGGGTGGCCCCTCTAAAGTTGAGGAAACATATGATTTTTTGTATCAATTATTTGCCGATAATGACCTAATTCCCATTAGTGCTAAGTATCAGAAGACAATTGCTAAATATATTGCTAAGTTTCGTACCCCCAAGATAGAGAAGCAATATAGGGAAATTGGTGGGGGCTCCCCAATCCGGAAATGGTCTGAGTATCAAGCCACTGAGGTCTGTAAAATCTTAGATAAAACCTGTCCAGAAACGGCGCCTCATAAGCCTTACGTGGCGTTTCGTTACGCAAAGCCGCTAACCGCAGAAACTTATAAACAAATGCTAAAAGATGGCGTGAAGAAGGCAGTGGCCTTTTCTCAATATCCTCATTTCTCTTATTCCACTACCGGGTCATCCATCAACGAATTGTGGAGACAGATTAAGGCATTGGACTCCGAGAGATCTATATCTTGGTCGGTTATTGATCGTTGGCCTACAAATGAAGGTCTAATCAAGGCCTTCTCCGAAAATATCACCAAAAAACTACAAGAGTTTCCGCAACCTGTCAGAGACAAGGTTGTTTTATTGTTTTCCGCACATTCTCTACCCATGGATGTTGTTAACACCGGTGATGCCTACCCAGCTGAGGTAGCTGCGACGGTTTACAACATCATGCAAAAATTAAAGTTTAAAAACCCTTATAGGTTGGTTTGGCAATCCCAAGTTGGACCAAAACCATGGTTGGGAGCGCAGACAGCTGAAATTGCGGAATTTTTAGGCCCCAAAGTTGATGGCCTAATGTTTATTCCTATCGCCTTTACCTCTGATCATATTGAAACATTGCATGAAATTGACTTAGGCGTCATTGGGGAATCGGAATATAAGGATAAATTTAAGAGATGCGAATCTTTAAATGGCAACCAGACCTTTATTGAAGGCATGGCAGATCTCGTCAAAAGCCACTTACAGAGTAACCAACTCTATTCTAATCAACTACCTCTTGATTTTGCACTTGGCAAGTCCAATGATCCTGTAAAGGACCTTTCATTGGTATTTGGCAATCACGAATCTACTTGA","protein_sequence":"MLSRTIRTQGSFLRRSQLTITRSFSVTFNMQNAQKRSPTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHEST"},{"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, acting on the CH-CH group of donors"},{"category":"Function","description":" oxygen-dependent protoporphyrinogen 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":"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":[],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"},{"name":"Porphyrin Metabolism","kegg_map_id":null}],"gene_sequence":"ATGTTATTACCATTAACAAAGCTAAAACCGAGAGCAAAAGTTGCTGTTGTAGGGGGTGGCGTTTCTGGACTATGTTTTACTTATTTTTTAAGCAAGTTGAGACCGGATGTTGAAATCACACTGTTCGAATCGCAGAACAGAACTGGGGGTTGGATATATTCTTGTAACACAAGAGATATGAGTGGGAACCCAATTATGTTGGAGAAGGGACCCAGAACATTGAGGGGCGTATCAGACGGGACCGTTCTGATTATGGATACCCTTAAAGACTTGGGCAAGGAAGCAGTTATTCAAAGCATTGATAAAGGTTGCATTGCAGACAAAAAGTTTCTACTAGACCCCAGTGATAAACTCGTGCAGGTTCCTAATTCGATATCTACAACAGTAAAATTTCTGCTGAATCCGTTGGGAAAAGGACTCATCACGGGTATGATGGGAGAATGGTTCAGAAAAAAATCTCCACATCCTGGCCAAGACGAAAGTGTCGAATCCATTTGTGACAGAAGGTTTGGGAATAACTACATATCAAACAATATGATCAGTGCCTTACTAAGAGGTATCTATGGGGATGACGTTTCCCTATTAAGTGCCAAGAGAACGTTTAAGAAAATATACTACAATGAACTAAAGCACGGATCTAACACACAAGCTATGATTGATAATATGCGCGGAAAGTCAAGAAGTAAAAAAACTGAGAACCTGCACCAATCTTTAACTGGCTGCCTTAACGACTACTCAAATGCGTTTGGAAAAGACAGGTCAAAGTTATTAGACTTATCCAACACGCTAAAGAAATATCCCATGTTGGGTCTTGCTGGGGGACTAGAAACGTTTCCCAAGATAGTCAGAAATGCTTTGAACGAATTTAAAAACGTCAAAATAGTTACTGGGAACCCGGTTACGCAAATAATGAAACGCCCTGCTAACGAAACGACAATCGGATTGAAAGCGAAATCTGGCGACCAATACGAAACATTTGACCATTTAAGACTTACGATAACACCTCCCAAAATCGCTAAATTGCTACCGAAGGATCAAAATTCATTATCCAAGTTATTAGATGAGATACAATCAAACACAATAATTTTAGTTAATTATTATTTGCCAAACAAAGATGTAATAGATGCCGATCTACAAGGCTTTGGATACTTGGTTCCCAAATCCAATAAGAATCCAGGGAAATTGCTTGGTGTAATTTTCGATTCTGTTATCGAAAGGAATTTCAAACCACTTTTTGACAAACTCTCCACAAACCCAAACGCCCTCAACAAATATACAAAAGTGACTGCGATGATAGGAGGTTGTATGCTCAATGAACACGGTGTTCCTGTAGTGCCATCCAGGGAGGTAACCATTAATGCAGTCAAAGATGCGCTGAACAACCACCTCGGCATCAGTAACAAGGATCTGGAAGCTGGTCAGTGGGAATTCACTATCGCCGATAGATGTCTGCCAAGATTTCATGTAGGTTATGACGCATGGCAAGAAAGAGCTGAAAGGAAGTTGCAAGAATCTTACGGCCAAACAGTTTCTGTGGGGGGAATGGGATTTTCTAGAAGTCCCGGTGTCCCTGACGTTATTGTAGACGGCTTTAACGACGCCTTACAGCTAAGCAAATAA","protein_sequence":"MLLPLTKLKPRAKVAVVGGGVSGLCFTYFLSKLRPDVEITLFESQNRTGGWIYSCNTRDMSGNPIMLEKGPRTLRGVSDGTVLIMDTLKDLGKEAVIQSIDKGCIADKKFLLDPSDKLVQVPNSISTTVKFLLNPLGKGLITGMMGEWFRKKSPHPGQDESVESICDRRFGNNYISNNMISALLRGIYGDDVSLLSAKRTFKKIYYNELKHGSNTQAMIDNMRGKSRSKKTENLHQSLTGCLNDYSNAFGKDRSKLLDLSNTLKKYPMLGLAGGLETFPKIVRNALNEFKNVKIVTGNPVTQIMKRPANETTIGLKAKSGDQYETFDHLRLTITPPKIAKLLPKDQNSLSKLLDEIQSNTIILVNYYLPNKDVIDADLQGFGYLVPKSNKNPGKLLGVIFDSVIERNFKPLFDKLSTNPNALNKYTKVTAMIGGCMLNEHGVPVVPSREVTINAVKDALNNHLGISNKDLEAGQWEFTIADRCLPRFHVGYDAWQERAERKLQESYGQTVSVGGMGFSRSPGVPDVIVDGFNDALQLSK"}]}