{"ymdb_id":"YMDB00249","created_at":"2011-05-29T17:58:31.000Z","updated_at":"2016-09-08T18:35:14.000Z","name":"Sirohydrochlorin","cas":"65207-12-7","state":null,"melting_point":null,"description":"Sirohydrochlorin is an intermediate in the last step of 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":"18023","hmdb_id":null,"kegg_id":"C02463","pubchem_id":"196427","cs_id":"24808091","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"3-[(4S,5S,9S,10S)-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(21),2,6,8(23),11,13,15,17,19-nonaen-4-yl]propanoic acid","traditional_iupac":"sirohydrochlorin","logp":"3.116881802","pka":"3.4318325811550707","alogps_solubility":"2.52e-02 g/l","alogps_logp":"1.04","alogps_logs":"-4.54","acceptor_count":"18","donor_count":"10","rotatable_bond_count":"20","polar_surface_area":"355.76","refractivity":"209.3843000000002","polarizability":"89.44342006533834","formal_charge":"0","physiological_charge":"-8","pka_strongest_basic":null,"pka_strongest_acidic":"3.05614721406891","bioavailability":"0","number_of_rings":"5","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrapropionic acid","Dihydrosirohydrochlorin","Precorrin 2","Sirohydrochlorin"],"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":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":"2011-05-27T01:53:37.000Z","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"}]}