{"ymdb_id":"YMDB00636","created_at":"2011-05-29T18:38:19.000Z","updated_at":"2016-09-08T18:35:43.000Z","name":"decaprenyl diphosphate","cas":null,"state":null,"melting_point":null,"description":"Decaprenyl diphosphate is a prenol lipid, specifically an isoprenoid-disphosphate. Prenol lipids are synthesized from the 5-carbon precursors isopentenyl diphosphate and dimethylallyl diphosphate that are produced mainly via the mevalonic acid pathway. Simple isoprenoids like Decaprenyl diphosphate are formed by the successive addition of C5 units.[Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"lipid particle","synthesis_reference":null,"chebi_id":"53043","hmdb_id":null,"kegg_id":"C04509","pubchem_id":"46173330","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"({[(3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid","traditional_iupac":"decaprenyl diphosphate","logp":"15.234732985666664","pka":"3.1843406094078315","alogps_solubility":"3.23e-04 g/l","alogps_logp":"8.90","alogps_logs":"-6.43","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"32","polar_surface_area":"113.29000000000002","refractivity":"263.34870000000006","polarizability":"103.91499821810635","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":["di-trans,poly-cis-Decaprenyl diphosphate","ditrans,heptacis-Decaprenyl diphosphate"],"pathways":[],"growth_conditions":[],"references":[{"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":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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Mediates the second step in the final reaction sequence of coenzyme Q (CoQ) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB","reactions":[{"id":1645,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2764,"direction":"\u003e","locations":"Mitochondrion inner membrane; Multi-pass membrane protein","altext":"A polyprenyl diphosphate + 4-hydroxybenzoate = diphosphate + a 4-hydroxy-3-polyprenylbenzoate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"92-112;114-133;170-191;193-210;229-249;298-318","pdb_id":null,"cellular_location":"Mitochondrion inner membrane; Multi-pass membrane protein","genbank_gene_id":"AY693097","genbank_protein_id":"51013645","gene_card_id":"COQ2","chromosome_location":"chromosome 14","locus":"YNR041C","synonyms":["PHB:polyprenyltransferase"],"enzyme_classes":["2.5.1.39"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" membrane part"},{"category":"Component","description":" intrinsic to membrane"},{"category":"Component","description":" integral to membrane"},{"category":"Function","description":" transferase activity, transferring alkyl or aryl (other than methyl) groups"},{"category":"Function","description":" prenyltransferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" biosynthetic process"}],"pfams":[{"name":"UbiA","identifier":"PF01040"}],"pathways":[],"gene_sequence":"ATGTTTATTTGGCAGAGAAAGAGTATTTTACTAGGGAGGTCCATTCTGGGCAGCGGCCGAGTTACCGTTGCTGGAATCATTGGAAGCAGCAGAAAGAGATATACGTCTTCTTCCTCCTCCTCCTCCTCCCCTTCCTCGAAAGAATCAGCACCTGTGTTTACGTCGAAAGAGTTGGAAGTTGCAAGAAAGGAAAGATTGGATGGACTGGGACCGTTCGTGTCTCGGCTGCCTAAGAAATGGATACCGTATGCGGAGCTGATGAGGCTAGAGAAACCCGTGGGCACGTGGCTGTTATATTTGCCCTGCAGTTGGTCTATACTTATGGGAGCCATGATGCAAGGTGCTACATTGAGCGCAACAGCTGGTATGTTGGGTATTTTCGGTGTAGGTGCATTGGTAATGAGAGGTGCTGGCTGCACCATCAACGATTTTTTGGATAGAAAGTTGGATCAAAGAGTTATCAGGTCCGTCGAGAGGCCTATCGCCTCTGGTAGAGTGAGCCCCCGTCGGGCGTTAGTATTCTTGGGGGCTCAAACTCTTGTTGGAATGGGCGTTCTATCTTTGCTTCCTGCGCAGTGTTGGTGGCTAGGCCTTGCATCGTTACCTATTGTGTTCACATACCCTTTGTTTAAGCGGTTTACGTACTATCCTCAAGCTGCATTAAGTGCATGTTTCAATTGGGGAGCGTTACTTGGGTTTCCTGCCATGGGTGTAATGAGCTGGCCTACAATGATACCTTTGTACCTGAGCAGTTACTTGTGGTGTATGACTTACGATACTATATACGCACACCAGGATAAAAAGTTTGACATCAAGACTGGAATCAAGTCTACCGCTTTGGCTTGGGGTCCACGCACAAAGTCTATCATGAAGGCCATGTCCGCGTCTCAAATCGCACTGTTAGCTGTCGCCGGCTTGAACAGTGGGTTGTTATGGGGGCCTGGGTTCATTGGTGGACTAGGAGTCTTCGCTTATAGACTCTTCAGCATGATAAAGAAAGTGGATCTTGACAATCCTAAAAACTGCTGGAAGTATTTTAATGCAAATATCAACACCGGACTTTACTTTACGTACGCCTTGGCAGTCGACTACATCTTGAGACTGTTTGGATTCTTGTAG","protein_sequence":"MFIWQRKSILLGRSILGSGRVTVAGIIGSSRKRYTSSSSSSSSPSSKESAPVFTSKELEVARKERLDGLGPFVSRLPKKWIPYAELMRLEKPVGTWLLYLPCSWSILMGAMMQGATLSATAGMLGIFGVGALVMRGAGCTINDFLDRKLDQRVIRSVERPIASGRVSPRRALVFLGAQTLVGMGVLSLLPAQCWWLGLASLPIVFTYPLFKRFTYYPQAALSACFNWGALLGFPAMGVMSWPTMIPLYLSSYLWCMTYDTIYAHQDKKFDIKAGIKSTALAWGPRTKSIMKAMSASQIALLAVAGLNSGLLWGPGFIGGLGVFAYRLFSMIKKVDLDNPKNCWKYFNANINTGLYFTYALAVDYILRLFGFL"}]}