{"ymdb_id":"YMDB00614","created_at":"2011-05-29T18:36:15.000Z","updated_at":"2016-09-08T18:35:41.000Z","name":"nonaprenyl diphosphate","cas":null,"state":null,"melting_point":null,"description":"Nonaprenyl diphosphate is an intermediate in ubiquinol-9 biosynthesis (eukaryotic) pathway. [Biocyc PWY-5871]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"lipid particle;cytoplasm","synthesis_reference":null,"chebi_id":"53044","hmdb_id":null,"kegg_id":"C04145","pubchem_id":"25244754","cs_id":"24808121","foodb_id":null,"wikipedia_link":null,"biocyc_id":"SOLANESYL-PYROPHOSPHATE","iupac":"{[hydroxy({[(2Z,6Z,10Z,14Z,18Z,22Z,26E,30E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]oxy})phosphoryl]oxy}phosphonic acid","traditional_iupac":"solanesyl-PP","logp":"13.575018710666667","pka":"3.2043406094078315","alogps_solubility":"3.19e-04 g/l","alogps_logp":"8.35","alogps_logs":"-6.39","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"29","polar_surface_area":"113.29","refractivity":"239.54610000000014","polarizability":"91.57773515670581","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":null,"pka_strongest_acidic":"1.7672186885241006","bioavailability":"0","number_of_rings":"0","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["all-trans-Nonaprenyl diphosphate","Solanesyl diphosphate","Solanesyl pyrophosphate"],"pathways":[{"name":"Terpenoid backbone biosynthesis","kegg_map_id":"00900"},{"name":"Ubiquinone and other terpenoid-quinone biosynthesis","kegg_map_id":"00130"}],"growth_conditions":[],"references":[{"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":1763050,"citation":"He, B., Chen, P., Chen, S. Y., Vancura, K. L., Michaelis, S., Powers, S. (1991). \"RAM2, an essential gene of yeast, and RAM1 encode the two polypeptide components of the farnesyltransferase that prenylates a-factor and Ras proteins.\" Proc Natl Acad Sci U S A 88:11373-11377."},{"pubmed_id":9858571,"citation":"Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J., Nakano, A. (1999). \"The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis.\" Mol Cell Biol 19:471-483."},{"pubmed_id":12702274,"citation":"Grabinska, K., Palamarczyk, G. (2002). \"Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase.\" FEMS Yeast Res 2:259-265."}],"proteins":[{"created_at":"2011-05-27T03:49:37.000Z","updated_at":"2011-07-22T17:54:30.000Z","name":"Putative dehydrodolichyl diphosphate synthase","uniprot_id":"Q03175","uniprot_name":"SRT1_YEAST","enzyme":true,"transporter":false,"gene_name":"SRT1","num_residues":343,"molecular_weight":"40199.69922","theoretical_pi":"10.03","general_function":"Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups","specific_function":"Could be a cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (ipp) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (DeDol- PP)","reactions":[{"id":1392,"direction":"\u003c\u003e","locations":"lipid 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farnesyltransferase subunit beta","uniprot_id":"P22007","uniprot_name":"FNTB_YEAST","enzyme":true,"transporter":false,"gene_name":"RAM1","num_residues":431,"molecular_weight":"48189.39844","theoretical_pi":"6.35","general_function":"Involved in catalytic activity","specific_function":"Catalyzes the transfer of a farnesyl moiety from farnesyl pyrophosphate to a cysteine at the fourth position from the C-terminus of several proteins such as a-factor and RAS. The beta subunit is responsible for peptide-binding","reactions":[{"id":2761,"direction":"\u003e","locations":"","altext":"Farnesyl diphosphate + protein-cysteine = S-farnesyl protein + diphosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"M22753","genbank_protein_id":"171420","gene_card_id":"RAM1","chromosome_location":"chromosome 4","locus":"YDL090C","synonyms":["FTase-beta","CAAX farnesyltransferase subunit beta","Ras proteins prenyltransferase subunit beta"],"enzyme_classes":["2.5.1.58"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" Not Available"}],"pfams":[{"name":"Prenyltrans","identifier":"PF00432"}],"pathways":[],"gene_sequence":"ATGCGACAGAGAGTAGGAAGGTCCATAGCTAGGGCTAAATTTATAAATACTGCCTTATTAGGAAGAAAGAGACCAGTTATGGAAAGAGTCGTCGATATAGCGCATGTAGATTCAAGTAAAGCAATCCAACCATTGATGAAGGAACTAGAAACCGACACTACAGAAGCACGATACAAAGTACTACAAAGTGTATTAGAGATATACGATGATGAAAAGAATATAGAACCTGCTCTCACGAAAGAGTTTCACAAAATGTACTTGGATGTCGCTTTTGAGATATCGTTACCTCCACAAATGACAGCACTAGATGCTTCACAACCGTGGATGCTATATTGGATTGCTAACTCATTGAAGGTAATGGACAGAGACTGGCTTTCAGATGACACCAAAAGAAAAATTGTAGATAAGCTCTTTACTATTAGTCCTTCAGGAGGACCCTTTGGTGGAGGTCCTGGCCAATTATCTCATTTGGCCAGCACTTATGCTGCAATTAATGCTCTCTCCCTTTGCGATAACATAGATGGATGCTGGGACAGAATTGATCGAAAAGGAATTTACCAATGGCTGATATCGTTGAAAGAGCCTAATGGAGGATTCAAGACCTGTTTAGAAGTCGGAGAAGTGGATACAAGAGGTATATACTGTGCCTTGAGCATAGCAACCTTATTAAATATTCTTACAGAAGAGCTTACAGAAGGTGTGTTAAACTATTTGAAAAATTGTCAAAATTATGAAGGTGGATTCGGCAGTTGTCCTCACGTAGATGAGGCACACGGAGGCTATACTTTCTGTGCTACAGCTAGTCTAGCAATTTTAAGGTCCATGGACCAAATAAATGTTGAAAAGCTTTTAGAATGGTCTAGTGCTCGTCAATTGCAAGAAGAACGAGGATTTTGCGGAAGGAGCAACAAACTTGTTGACGGTTGCTATAGTTTTTGGGTTGGAGGTTCGGCTGCCATTCTTGAAGCTTTTGGATATGGCCAATGCTTCAACAAACATGCTCTTCGGGACTACATATTGTACTGTTGCCAAGAAAAAGAGCAACCTGGTTTGAGAGATAAACCAGGGGCCCACTCAGACTTTTACCATACAAATTATTGCCTATTAGGACTGGCTGTTGCGGAAAGTTCATACAGTTGCACTCCTAATGATTCTCCACATAATATTAAGTGTACTCCAGACCGCCTAATTGGATCATCGAAACTTACTGATGTCAACCCTGTCTATGGTTTACCAATAGAAAATGTAAGAAAAATTATCCACTACTTTAAATCCAATTTATCTTCTCCAAGTTAA","protein_sequence":"MRQRVGRSIARAKFINTALLGRKRPVMERVVDIAHVDSSKAIQPLMKELETDTTEARYKVLQSVLEIYDDEKNIEPALTKEFHKMYLDVAFEISLPPQMTALDASQPWMLYWIANSLKVMDRDWLSDDTKRKIVDKLFTISPSGGPFGGGPGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNILTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCGRSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAESSYSCTPNDSPHNIKCTPDRLIGSSKLTDVNPVYGLPIENVRKIIHYFKSNLSSPS"}]}