{"ymdb_id":"YMDB00141","created_at":"2011-05-29T16:00:54.000Z","updated_at":"2016-09-08T18:35:05.000Z","name":"ADP-ribose 1\"-2\" cyclic phosphate ","cas":null,"state":"Solid","melting_point":null,"description":"ADP-ribose 1''-2''cyclic phosphate is a cyclic phosphate nucleotide that arises from tRNA processing.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":null,"chebi_id":null,"hmdb_id":"HMDB11671","kegg_id":null,"pubchem_id":"44415073","cs_id":"23106974","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}[({[(5R)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphinic acid","traditional_iupac":"[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy({[(5R)-2,6-dihydroxy-2-oxo-tetrahydro-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy(hydroxy)phosphoryl}oxy)phosphinic acid","logp":"-6.324328954886622","pka":"1.9415909556394526","alogps_solubility":"4.97e+00 g/l","alogps_logp":"-1.28","alogps_logs":"-2.10","acceptor_count":"15","donor_count":"7","rotatable_bond_count":"9","polar_surface_area":"306.82","refractivity":"118.21719999999996","polarizability":"49.45665077153953","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"4.996835503117071","pka_strongest_acidic":"1.350523039338686","bioavailability":"0","number_of_rings":"5","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["adenosine diphosphate ribose 1\"-2\" cyclic phosphate","ADP ribose 1'',2''-phosphate","ADP-ribose 1 ,2 -cyclic phosphate","ADP-ribose 1' ,2' -cyclic phosphate"],"pathways":[],"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":15611300,"citation":"Steiger, M. A., Jackman, J. E., Phizicky, E. M. (2005). \"Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism.\" RNA 11:99-106."},{"pubmed_id":8392224,"citation":"Culver, G. M., McCraith, S. M., Zillmann, M., Kierzek, R., Michaud, N., LaReau, R. D., Turner, D. H., Phizicky, E. M. (1993). \"An NAD derivative produced during transfer RNA splicing: ADP-ribose 1\"-2\" cyclic phosphate.\" Science 261:206-208."},{"pubmed_id":15684411,"citation":"Shull, N. P., Spinelli, S. L., Phizicky, E. M. (2005). \"A highly specific phosphatase that acts on ADP-ribose 1''-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae.\" Nucleic Acids Res 33:650-660."}],"proteins":[{"created_at":"2011-05-27T01:45:12.000Z","updated_at":"2011-05-29T05:06:34.000Z","name":"tRNA 2'-phosphotransferase","uniprot_id":"Q12272","uniprot_name":"TPT1_YEAST","enzyme":true,"transporter":false,"gene_name":"TPT1","num_residues":230,"molecular_weight":"26196.19922","theoretical_pi":"9.81","general_function":"Involved in transferase activity, transferring phosphorus-containing groups","specific_function":"Catalyzes the last step of tRNA splicing, the transfer of the splice junction 2'-phosphate from ligated tRNA to NAD to produce ADP-ribose 1''-2'' cyclic phosphate","reactions":[{"id":2641,"direction":"\u003e","locations":null,"altext":"2'-phospho-[ligated tRNA] + NAD(+) = mature tRNA + ADP ribose 1'',2''-phosphate + nicotinamide + H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"Z48149","genbank_protein_id":"663252","gene_card_id":"TPT1","chromosome_location":"chromosome 15","locus":"YOL102C","synonyms":[],"enzyme_classes":["2.7.1.160"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Process","description":" cellular macromolecule metabolic process"},{"category":"Process","description":" RNA metabolic process"},{"category":"Process","description":" RNA processing"},{"category":"Process","description":" RNA splicing"},{"category":"Process","description":" RNA splicing, via endonucleolytic cleavage and ligation"},{"category":"Process","description":" tRNA splicing, via endonucleolytic cleavage and ligation"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" macromolecule metabolic process"}],"pfams":[{"name":"PTS_2-RNA","identifier":"PF01885"}],"pathways":[],"gene_sequence":"ATGCGCCAGGTACTACAAAAAGATAAAAGGGATGTACAGCTTTCCAAAGCTTTATCATATCTGCTTCGACATACAGCGGTGAAAGAAAAGTTGACTATTGACTCAAACGGTTATACACCGCTGAAAGAACTATTGTCTCATAATAGATTGAAAACTCATAAATGTACGGTGGATGATATCCATCGCATTGTTAAGGAAAATGACAAACAACGCTTTCATATAAAAACGTTAGGAGCGGACGAAGAATGGATCTGTGCTACTCAGGGACATTCAATCAAATCGATTCAGCCATCAGATGAGGTTCTCGTACCAATTACTGAAGCGTCGCAGTTACCACAGGAACTAATTCATGGAACAAATCTTCAATCTGTCATAAAGATTATTGAATCCGGAGCAATATCACCAATGAGTAGAAATCATGTCCATTTATCGCCGGGGATGTTGCACGCGAAGGGAGTTATTAGTGGAATGCGTTCTTCAAGTAACGTCTATATTTTCATCGACTGCCATTCTCCATTATTCTTTCAAACTTTGAAAATGTTCAGGTCGCTCAATAATGTTTACTTAAGCAGCAGTATTCCCGTTGAATTGATCCAAAAAGTTGTAGTTAAAGGAAACTTGAAAGATGAGGAGAAGTTAGATACTTTAAGAAGAATTTTACACGAAAGAAACATACCGCTCGAAAAGATATAA","protein_sequence":"MRQVLQKDKRDVQLSKALSYLLRHTAVKEKLTIDSNGYTPLKELLSHNRLKTHKCTVDDIHRIVKENDKQRFHIKTLGADEEWICATQGHSIKSIQPSDEVLVPITEASQLPQELIHGTNLQSVIKIIESGAISPMSRNHVHLSPGMLHAKGVISGMRSSSNVYIFIDCHSPLFFQTLKMFRSLNNVYLSSSIPVELIQKVVVKGNLKDEEKLDTLRRILHERNIPLEKI"}]}