{"ymdb_id":"YMDB00977","created_at":"2011-06-03T16:59:12.000Z","updated_at":"2016-09-08T18:36:06.000Z","name":"Precorrin-2","cas":"82542-92-5","state":null,"melting_point":null,"description":"Precorrin-2 is an intermediate in the siroheme biosynthesis pathway. Siroheme is an iron-containing isobacteriochlorin, a modified tetrapyrrole similar in structure to both heme and chlorophyll. Siroheme is found as a prosthetic group of several enzymes, including sulfite and nitrite reductases, which catalyze the six-electron reductions of sulfite to sulfide and nitrite to ammonia, respectively. Siroheme biosynthesis starts by the same route as other tetrapyrroles, the synthesis of the intermediate uroporphyrinogen-III. [Biocyc PWY-5194]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"50602","hmdb_id":null,"kegg_id":"C02463","pubchem_id":"25245987","cs_id":"24808156","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"3-[(4S,5S,6Z,9S,10S,11Z)-9,15,19-tris(2-carboxyethyl)-5,10,14,20-tetrakis(carboxymethyl)-5,10-dimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),2,6,8(23),11,13,15,18-octaen-4-yl]propanoic acid","traditional_iupac":"3-[(4S,5S,6Z,9S,10S,11Z)-9,15,19-tris(2-carboxyethyl)-5,10,14,20-tetrakis(carboxymethyl)-5,10-dimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),2,6,8(23),11,13,15,18-octaen-4-yl]propanoic acid","logp":"1.0931127170000008","pka":"3.286335191141454","alogps_solubility":"3.43e-02 g/l","alogps_logp":"1.07","alogps_logs":"-4.40","acceptor_count":"18","donor_count":"11","rotatable_bond_count":"20","polar_surface_area":"354.36999999999995","refractivity":"217.2320000000002","polarizability":"89.12937976901685","formal_charge":"0","physiological_charge":"-7","pka_strongest_basic":null,"pka_strongest_acidic":"2.9114023752442866","bioavailability":"0","number_of_rings":"5","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["15,23-Dihydrosirohydrochlorin","Dihydrosirohydrochlorin","Precorrin 2"],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"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":10051442,"citation":"Raux, E., McVeigh, T., Peters, S. E., Leustek, T., Warren, M. J. (1999). \"The role of Saccharomyces cerevisiae Met1p and Met8p in sirohaem and cobalamin biosynthesis.\" Biochem J 338 ( Pt 3):701-708."},{"pubmed_id":11980703,"citation":"Schubert, H. L., Raux, E., Brindley, A. A., Leech, H. K., Wilson, K. S., Hill, C. P., Warren, M. J. (2002). \"The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase.\" EMBO J 21:2068-2075."}],"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":" heme biosynthetic process"},{"category":"Process","description":" siroheme biosynthetic process"},{"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"},{"category":"Process","description":" oxidation reduction"}],"pfams":[{"name":"TP_methylase","identifier":"PF00590"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGGTACGAGACTTAGTGACATTGCCTTCATCACTGCCCTTGATTACTGCTGGTTTTGCTACTGATCAGGTTCATTTGCTTATTGGTACAGGGTCCACGGACTCAGTAAGCGTTTGTAAGAATAGAATCCACTCCATTTTGAATGCTGGTGGTAATCCCATAGTAGTGAATCCCTCGTCACCAAGCCATACTAAACAATTACAATTGGAATTTGGTAAGTTTGCAAAGTTCGAAATAGTAGAAAGGGAGTTTAGGTTATCTGATTTAACTACTTTGGGGAGAGTTCTGGTATGCAAGGTAGTGGATAGAGTATTCGTAGATCTACCCATAACACAAAGTCGCCTATGCGAGGAGATCTTTTGGCAATGCCAAAAACTGAGAATTCCCATAAATACATTCCACAAACCAGAGTTTTCTACCTTCAATATGATTCCTACGTGGGTCGACCCAAAAGGAAGTGGTTTACAAATCTCAGTTACTACGAATGGGAATGGATACATCTTGGCAAACAGGATAAAAAGAGATATAATATCACACTTACCTCCAAACATATCTGAGGTGGTGATAAACATGGGGTATTTGAAAGACCGTATTATAAACGAAGACCATAAGGCCTTGTTAGAGGAAAAGTACTACCAGACTGACATGTCATTACCTGGATTTGGCTACGGCTTAGATGAGGACGGTTGGGAGAGCCATAAGTTTAATAAGCTAATTCGTGAATTTGAAATGACCAGTAGAGAACAGAGACTTAAGAGAACCAGATGGTTATCTCAGATAATGGAGTATTACCCGATGAACAAGCTGAGTGACATCAAGTTGGAAGATTTCGAGACTTCATCTTCTCCAAATAAAAAGACAAAGCAGGAAACTGTCACAGAGGGTGTAGTACCTCCTACCGATGAAAATATTGAAAACGGTACAAAACAACTACAATTATCGGAAGTGAAAAAAGAGGAGGGACCTAAAAAACTAGGGAAGATTTCTTTAGTCGGAAGTGGTCCAGGCTCGGTATCTATGCTAACGATAGGTGCATTACAAGAAATAAAGTCTGCAGATATAATACTGGCAGATAAACTGGTACCGCAAGCCATTTTAGATTTAATACCTCCAAAAACTGAAACCTTCATAGCCAAAAAATTTCCCGGTAATGCAGAACGAGCACAACAGGAATTACTAGCTAAAGGTTTAGAATCGTTGGATAATGGATTGAAAGTAGTCCGTTTGAAGCAAGGTGATCCGTATATTTTTGGCCGTGGTGGCGAGGAATTTAATTTCTTCAAAGATCACGGATATATTCCTGTGGTTTTACCGGGCATAAGCTCATCCCTAGCTTGTACTGTATTGGCTCAGATACCCGCTACTCAACGTGATATAGCAGACCAAGTGCTCATATGTACTGGGACTGGGAGAAAGGGCGCTCTGCCTATAATTCCTGAATTTGTTGAAAGCAGAACCACCGTCTTTCTAATGGCACTGCATCGCGCCAACGTTCTGATCACGGGATTATTGAAGCATGGCTGGGATGGTGATGTCCCCGCTGCAATTGTCGAGAGAGGATCGTGCCCTGACCAGCGTGTTACTAGAACTCTTCTTAAATGGGTACCAGAAGTCGTGGAGGAGATTGGTTCAAGGCCCCCCGGTGTCTTGGTTGTAGGCAAGGCTGTGAATGCATTGGTTGAAAAAGATCTGATAAATTTTGACGAATCAAGAAAATTTGTCATTGATGAAGGTTTTAGAGAATTTGAGGTTGATGTAGATAGTCTATTTAAGTTATACTAA","protein_sequence":"MVRDLVTLPSSLPLITAGFATDQVHLLIGTGSTDSVSVCKNRIHSILNAGGNPIVVNPSSPSHTKQLQLEFGKFAKFEIVEREFRLSDLTTLGRVLVCKVVDRVFVDLPITQSRLCEEIFWQCQKLRIPINTFHKPEFSTFNMIPTWVDPKGSGLQISVTTNGNGYILANRIKRDIISHLPPNISEVVINMGYLKDRIINEDHKALLEEKYYQTDMSLPGFGYGLDEDGWESHKFNKLIREFEMTSREQRLKRTRWLSQIMEYYPMNKLSDIKLEDFETSSSPNKKTKQETVTEGVVPPTDENIENGTKQLQLSEVKKEEGPKKLGKISLVGSGPGSVSMLTIGALQEIKSADIILADKLVPQAILDLIPPKTETFIAKKFPGNAERAQQELLAKGLESLDNGLKVVRLKQGDPYIFGRGGEEFNFFKDHGYIPVVLPGISSSLACTVLAQIPATQRDIADQVLICTGTGRKGALPIIPEFVESRTTVFLMALHRANVLITGLLKHGWDGDVPAAIVERGSCPDQRVTRTLLKWVPEVVEEIGSRPPGVLVVGKAVNALVEKDLINFDESRKFVIDEGFREFEVDVDSLFKLY"},{"created_at":"2011-05-27T01:53:37.000Z","updated_at":"2011-05-27T15:01:16.000Z","name":"Siroheme biosynthesis protein MET8","uniprot_id":"P15807","uniprot_name":"MET8_YEAST","enzyme":true,"transporter":false,"gene_name":"MET8","num_residues":274,"molecular_weight":"31917.40039","theoretical_pi":"6.26","general_function":"Involved in binding","specific_function":"Catalyzes the conversion of precorrin-2 into siroheme. This reaction consist of the NAD-dependent oxidation of precorrin- 2 into sirohydrochlorin and its subsequent ferrochelation into siroheme","reactions":[{"id":1967,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1968,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2646,"direction":"\u003e","locations":null,"altext":"Precorrin-2 + NAD(+) = sirohydrochlorin + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":2647,"direction":"\u003e","locations":null,"altext":"Siroheme + 2 H(+) = sirohydrochlorin + Fe(2+).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1KYQ","cellular_location":null,"genbank_gene_id":"X17271","genbank_protein_id":"3934","gene_card_id":"MET8","chromosome_location":"chromosome 2","locus":"YBR213W","synonyms":["Precorrin-2 dehydrogenase","Sirohydrochlorin ferrochelatase"],"enzyme_classes":["1.3.1.76","4.99.1.4"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"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":[],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGGTCAAATCGCTACAGCTAGCCCATCAATTAAAAGACAAGAAAATACTACTAATCGGAGGCGGAGAAGTCGGCTTGACAAGGTTATATAAGCTGATACCTACAGGTTGCAAGCTGACTTTAGTATCTCCTGACCTACACAAATCCATTATTCCGAAGTTTGGAAAATTCATCCAGAACGAGGATCAGCCCGACTACAGAGAAGACGCTAAACGCTTTATCAATCCGAACTGGGACCCCACGAAGAATGAAATTTACGAGTACATCCGCAGTGACTTCAAAGACGAATACCTCGACCTAGAAGACGAGAACGACGCGTGGTACATAATAATGACCTGTATACCCGACCACCCTGAAAGCGCAAGAATATATCACCTTTGTAAGGAAAGATTCGGTAAGCAGCAGCTGGTCAATGTGGCGGACAAACCTGATCTCTGTGACTTTTATTTCGGCGCCAACCTGGAGATAGGAGACCGTCTACAGATTCTGATCTCTACCAACGGCCTTTCTCCGCGCTTTGGCGCTCTAGTAAGAGATGAGATCCGTAACTTATTCACACAAATGGGGGATCTGGCGCTGGAGGACGCTGTCGTCAAACTAGGTGAGCTGAGAAGAGGAATTAGGCTGCTGGCACCAGACGACAAGGATGTCAAGTACCGCATGGATTGGGCCAGACGCTGCACAGACCTCTTCGGCATTCAGCACTGCCACAACATCGACGTAAAACGTCTGCTGGATCTTTTCAAGGTCATGTTTCAAGAACAGAACTGTTCCTTGCAGTTCCCTCCCAGAGAACGGTTGCTTAGCGAGTACTGCTCGTCTTGA","protein_sequence":"MVKSLQLAHQLKDKKILLIGGGEVGLTRLYKLIPTGCKLTLVSPDLHKSIIPKFGKFIQNEDQPDYREDAKRFINPNWDPTKNEIYEYIRSDFKDEYLDLEDENDAWYIIMTCIPDHPESARIYHLCKERFGKQQLVNVADKPDLCDFYFGANLEIGDRLQILISTNGLSPRFGALVRDEIRNLFTQMGDLALEDAVVKLGELRRGIRLLAPDDKDVKYRMDWARRCTDLFGIQHCHNIDVKRLLDLFKVMFQEQNCSLQFPPRERLLSEYCSS"}]}