{"ymdb_id":"YMDB00349","created_at":"2011-05-29T18:08:27.000Z","updated_at":"2016-10-18T17:11:27.000Z","name":"Adenosine 3',5'-diphosphate","cas":"1053-73-2","state":"Solid","melting_point":"","description":"Adenosine 3',5'-diphosphate (PAP) is a nucleotide closely related to ADP. It has two phosphate groups attached to the 5' and 3' positions of the pentose sugar ribose. Phosphatases converting 3'-phosphoadenosine 5'-phosphate (PAP) into adenosine 5'-phosphate are of fundamental importance in living cells as the accumulation of PAP is toxic to several cellular systems.","experimental_water_solubility":"614.5 mg/mL [HMP experimental]","experimental_logp_hydrophobicity":"","location":"extracellular;mitochondrion;cytoplasm","synthesis_reference":"Tsunako, Mitsutomo; Kotone, Akira.  Preparation of nucleoside-2',5'- and 3',5'-diphosphoric acids.    Jpn. Kokai Tokkyo Koho  (1991),     13 pp.","chebi_id":"17985","hmdb_id":"HMDB00061","kegg_id":"C00054","pubchem_id":"159296","cs_id":"140102","foodb_id":null,"wikipedia_link":null,"biocyc_id":"3-5-ADP","iupac":"{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"adenosine 3',5'-bisphosphate","logp":"-4.800569399208871","pka":"1.3803079575190602","alogps_solubility":"3.33e+00 g/l","alogps_logp":"-1.63","alogps_logs":"-2.11","acceptor_count":"12","donor_count":"6","rotatable_bond_count":"6","polar_surface_area":"232.59999999999994","refractivity":"84.94139999999997","polarizability":"34.284901391907525","formal_charge":"0","physiological_charge":"-4","pka_strongest_basic":"3.9159304731893356","pka_strongest_acidic":"0.7047720713348022","bioavailability":"0","number_of_rings":"3","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["3-Phosphoadenosine 5-phosphate","3,5-ADP","3,5-Diphosphoadenosine","3'-Phosphoryl-AMP","5-(dihydrogen phosphate) 3-Adenylate","5-(dihydrogen phosphate)3'-Adenylic acid","Adenosine 3,5-bis","Adenosine 3,5-bisphosphate","Adenosine 3,5-diphosphic acid","adenosine 3',5'-bisphosphate"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Sulfur metabolism","kegg_map_id":"00920"},{"name":"Pantothenate and CoA biosynthesis","kegg_map_id":"00770"}],"growth_conditions":[{"growth_media":"Glucose limited aerobic culture","concentration":"1.3","concentration_units":"umol/g DW","error":"0.0"}],"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":2203779,"citation":"Thomas, D., Barbey, R., Surdin-Kerjan, Y. (1990). \"Gene-enzyme relationship in the sulfate assimilation pathway of Saccharomyces cerevisiae. Study of the 3'-phosphoadenylylsulfate reductase structural gene.\" J Biol Chem 265:15518-15524."}],"proteins":[{"created_at":"2011-05-26T16:08:08.000Z","updated_at":"2011-07-22T17:53:56.000Z","name":"Mitochondrial holo-[acyl-carrier-protein] synthase","uniprot_id":"Q12036","uniprot_name":"PPT2_YEAST","enzyme":true,"transporter":false,"gene_name":"PPT2","num_residues":173,"molecular_weight":"19973.0","theoretical_pi":"8.57","general_function":"Involved in magnesium ion binding","specific_function":"Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of mitochondrial acyl-carrier-protein","reactions":[{"id":1248,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2412,"direction":"\u003e","locations":"Mitochondrion (Probable)","altext":"CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein].","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion (Probable)","genbank_gene_id":"AY558134","genbank_protein_id":"45270158","gene_card_id":"PPT2","chromosome_location":"chromosome 16","locus":"YPL148C","synonyms":["Mitochondrial holo-ACP synthase","4'-phosphopantetheinyl transferase PPT2","PPTase"],"enzyme_classes":["2.7.8.7"],"go_classes":[{"category":"Component","description":" organelle"},{"category":"Component","description":" membrane-bounded organelle"},{"category":"Component","description":" intracellular membrane-bounded organelle"},{"category":"Component","description":" mitochondrion"},{"category":"Function","description":" binding"},{"category":"Function","description":" holo-[acyl-carrier-protein] synthase activity"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" magnesium ion binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, for other substituted phosphate groups"},{"category":"Process","description":" post-translational protein modification"},{"category":"Process","description":" macromolecule biosynthetic process"},{"category":"Process","description":" protein-cofactor linkage"},{"category":"Process","description":" organic acid metabolic process"},{"category":"Process","description":" oxoacid metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" carboxylic acid metabolic process"},{"category":"Process","description":" macromolecule metabolic process"},{"category":"Process","description":" macromolecule modification"},{"category":"Process","description":" protein modification process"},{"category":"Process","description":" monocarboxylic acid metabolic process"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" fatty acid metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" fatty acid biosynthetic process"}],"pfams":[{"name":"ACPS","identifier":"PF01648"}],"pathways":[{"name":"Pantothenate and CoA biosynthesis","kegg_map_id":"00770"}],"gene_sequence":"ATGCCTCCAGTGATGAGTTTTGCATCGAGGAATATTGGACGTAAGATAGCAGGAGTGGGAGTTGACATTGTATACTTGCCAAGATTTGCACATATACTAGAGAAATATTCCCCATTCGACCCATGTGGCCGTTCTACCTTGAATAAAATAACACGGAAGTTCATGCATGAAAAGGAAAGATTTCATTTCAGTAATCTTCTCATCGAAGAAAACTGCTTAACTCCACGATTGCATGAATATATAGCGGGAGTTTGGGCTTTGAAGGAATGCTCATTGAAAGCGTTGTGTTGCTGTGTTTCAAAGCATGATCTACCTCCTGCCCAAGTACTGTACGCTGGAATGCTATATAAAACACAAACCGATACAGGTGTACCTCAGTTAGAGTTTGATAAGATGTTTGGAAAAAAGTATCCAAAGTATCAACAGCTCTCGAAAAACTACGATTCTCTCTTTTCCACTCATGAGTTTTTAGTTTCGCTATCCCATGATAAAGATTATTTAATTGCAGTAACAAACTTGGTAGAAAGAGAGTAA","protein_sequence":"MSFASRNIGRKIAGVGVDIVYLPRFAHILEKYSPFDPCGRSTLNKITRKFMHEKERFHFSNLLIEENCLTPRLHEYIAGVWALKECSLKALCCCVSKHDLPPAQVLYAGMLYKTQTDTGVPQLEFDKMFGKKYPKYQQLSKNYDSLFSTHEFLVSLSHDKDYLIAVTNLVERE"},{"created_at":"2011-05-26T18:34:18.000Z","updated_at":"2011-07-22T17:53:44.000Z","name":"3'(2'),5'-bisphosphate nucleotidase","uniprot_id":"P32179","uniprot_name":"HAL2_YEAST","enzyme":true,"transporter":false,"gene_name":"HAL2","num_residues":357,"molecular_weight":"39148.89844","theoretical_pi":"6.13","general_function":"Involved in 3'(2'),5'-bisphosphate nucleotidase activity","specific_function":"Converts adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS) and 3'(2')-phosphoadenosine 5'- phosphate (PAP) to AMP. Regulates the flux of sulfur in the sulfur-activation pathway by converting PAPS to APS. Involved in salt tolerance. Confers resistance to lithium","reactions":[{"id":1154,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2538,"direction":"\u003e","locations":"Cytoplasmic","altext":"Adenosine 3',5'-bisphosphate + H(2)O = adenosine 5'-phosphate + phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1KA1","cellular_location":"Cytoplasmic","genbank_gene_id":"AY500154","genbank_protein_id":"40786813","gene_card_id":"HAL2","chromosome_location":null,"locus":"YOL064C","synonyms":["3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrolase","DPNPase","Halotolerance protein HAL2"],"enzyme_classes":["3.1.3.7"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" nucleotidase activity"},{"category":"Function","description":" 3'(2'),5'-bisphosphate nucleotidase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on ester bonds"},{"category":"Function","description":" phosphoric ester hydrolase activity"},{"category":"Function","description":" phosphatase activity"},{"category":"Function","description":" inositol or phosphatidylinositol phosphatase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" sulfur metabolic process"}],"pfams":[{"name":"Inositol_P","identifier":"PF00459"}],"pathways":[{"name":"Sulfur metabolism","kegg_map_id":"00920"}],"gene_sequence":"ATGGCATTGGAAAGAGAATTATTGGTTGCAACTCAAGCTGTACGAAAGGCGTCTTTATTGACTAAGAGAATTCAATCTGAAGTGATTTCTCACAAGGACTCCACTACTATTACCAAGAGTGATAATTCTCCAGTAACCACAGGTGATTATGCTGCACAAACGATCATCATAAATGCTATCATGAGCAGTTTCCCTGATGATAAGGTGGTTGGTGAAGAATCCTCATCAGGATTGAGCGACGCATTCGTCTCAGGAATTTTAAACGAAATAAAAGCCAATGACGAAGTTTATAACAAGAATTATAAAAAGGATGATTTTCTGTTTACAAACGATCAGTTTCCGCTAAAATCTTTGGAGGACGTCAGGCAAATCATCGATTTCGGCAATTACGAAGGTGGTAGAAAAGGAAGATTTTGGTGTTTGGATCCTATTGACGGAACCAAGGGGTTTTTAAGAGGCGAACAGTTTGCAGTATGTCTGGCCTTAATTGTGGACGGTGTTGTTCAGCTTGGTTGTATTGGATGCCCCAACTTAGTTTTAAGTTCTTATGGGGCCCAAGATTTGAAAGGCCATGAGTCATTTGGTTATATCTTTCGTGCTGTTAGAGGTTTAGGTGCCTTCTATTCTCCATCTTCAGATGCAGAGTCATGGACCAAAATCCACGTTAGACACTTAAAAGACACTAAAGACATGATTACTTTAGAGGGAGTTGAAAAGGGACACTCCTCTCATGATGAACAAACTGCTATCAAAAACAAACTAAATATATCCAAATCTTTGCACTTGGATTCTCAAGCCAAGTACTGTTTGTTAGCATTGGGCTTAGCAGACGTATATTTACGTCTGCCTATCAAACTTTCTTACCAAGAAAAGATCTGGGACCATGCTGCAGGCAACGTTATTGTCCACGAAGCTGGTGGTGTCCATACAGATGCCATGGAAGATGTTCCTCTAGACTTCGGTAACGGTAGAACGCTAGCTACGAAGGGAGTTATAGCGTCAAGTGGCCCTCGCGAGTTACATGACTTGGTGGTGTCTACATCATGCGATGTCATTCAGTCAAGGAACGCCTAA","protein_sequence":"MALERELLVATQAVRKASLLTKRIQSEVISHKDSTTITKNDNSPVTTGDYAAQTIIINAIKSNFPDDKVVGEESSSGLSDAFVSGILNEIKANDEVYNKNYKKDDFLFTNDQFPLKSLEDVRQIIDFGNYEGGRKGRFWCLDPIDGTKGFLRGEQFAVCLALIVDGVVQLGCIGCPNLVLSSYGAQDLKGHESFGYIFRAVRGLGAFYSPSSDAESWTKIHVRHLKDTKDMITLEGVEKGHSSHDEQTAIKNKLNISKSLHLDSQAKYCLLALGLADVYLRLPIKLSYQEKIWDHAAGNVIVHEAGGIHTDAMEDVPLDFGNGRTLATKGVIASSGPRELHDLVVSTSCDVIQSRNA"},{"created_at":"2011-05-27T02:04:30.000Z","updated_at":"2011-05-27T15:01:16.000Z","name":"Phosphoadenosine phosphosulfate reductase","uniprot_id":"P18408","uniprot_name":"MET16_YEAST","enzyme":true,"transporter":false,"gene_name":"MET16","num_residues":261,"molecular_weight":"30380.09961","theoretical_pi":"5.8","general_function":"Involved in phosphoadenylyl-sulfate reductase (thioredoxin) activity","specific_function":"The NADP dependent reduction of PAPS into sulfite involves thioredoxin which probably plays the role of a thiol carrier","reactions":[{"id":2658,"direction":"\u003e","locations":null,"altext":"Adenosine 3',5'-bisphosphate + sulfite + thioredoxin disulfide = 3'-phosphoadenylyl sulfate + thioredoxin.","export":false,"pw_reaction_id":null,"source":null},{"id":14419,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006932","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY693236","genbank_protein_id":"51013923","gene_card_id":"MET16","chromosome_location":"chromosome 16","locus":"YPR167C","synonyms":["3'-phosphoadenylylsulfate reductase","PAPS reductase, thioredoxin dependent","PAdoPS reductase"],"enzyme_classes":["1.8.4.8"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" oxidoreductase activity, acting on a sulfur group of donors"},{"category":"Function","description":" phosphoadenylyl-sulfate reductase (thioredoxin) activity"},{"category":"Function","description":" oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Process","description":" sulfur amino acid metabolic process"},{"category":"Process","description":" sulfur amino acid biosynthetic process"},{"category":"Process","description":" cysteine biosynthetic process"},{"category":"Process","description":" sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin)"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" sulfur metabolic process"},{"category":"Process","description":" sulfate assimilation"}],"pfams":[{"name":"PAPS_reduct","identifier":"PF01507"}],"pathways":[{"name":"Sulfur metabolism","kegg_map_id":"00920"}],"gene_sequence":"ATGAAGACCTATCATTTGAATAATGATATAATTGTCACACAAGAACAGTTGGATCATTGGAATGAACAACTAATCAAGCTGGAAACGCCACAGGAGATTATTGCATGGTCTATCGTAACGTTTCCTCACCTTTTCCAAACCACTGCATTTGGTTTGACTGGCTTGGTTACTATCGATATGTTGTCAAAGCTATCTGAAAAATACTACATGCCAGAACTATTATTTATAGACACTTTGCACCATTTCCCACAAACTTTAACACTAAAAAACGAGATTGAGAAAAAATACTACCAGCCTAAAAATCAAACCATTCACGTATATAAGCCGGATGGATGTGAATCGGAGGCAGATTTTGCCTCGAAATACGGGGATTTCTTATGGGAGAAAGATGATGACAAGTACGATTATCTGGCCAAAGTGGAACCTGCACATCGTGCCTACAAAGAGCTACATATAAGTGCTGTGTTTACTGGTAGAAGAAAATCACAAGGTTCTGCCCGCTCCCAACTGTCGATTATTGAAATAGACGAACTTAATGGAATCTTAAAAATAAATCCATTGATCAATTGGACGTTCGAGCAGGTTAAACAGTATATAGATGCAAACAATGTACCATACAACGAACTTTTGGACCTTGGATATAGATCCATTGGTGATTACCATTCCACACAACCCGTCAAGGAAGGTGAAGATGAGAGAGCAGGAAGATGGAAGGGCAAGGCCAAGACCGAGTGTGGAATTCATGAAGCCAGCCGATTCGCGCAATTTTTAAAGCAAGATGCCTAG","protein_sequence":"MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRWKGKAKTECGIHEASRFAQFLKQDA"},{"created_at":"2011-05-27T07:01:34.000Z","updated_at":"2011-05-27T15:01:27.000Z","name":"L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase","uniprot_id":"P50113","uniprot_name":"LYS5_YEAST","enzyme":true,"transporter":false,"gene_name":"LYS5","num_residues":272,"molecular_weight":"30682.90039","theoretical_pi":"4.42","general_function":"Involved in magnesium ion binding","specific_function":"Catalyzes the transfer of a 4'-phosphopantetheine moiety from coenzyme A to a serine residue of acceptor proteins, such as alpha-aminoadipate reductase. Necessary for alpha-aminoadipate reductase activity","reactions":[{"id":2798,"direction":"\u003e","locations":null,"altext":"CoA-[4'-phosphopantetheine] + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein].","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY692861","genbank_protein_id":"51013173","gene_card_id":"LYS5","chromosome_location":"chromosome 7","locus":"YGL154C","synonyms":["AASD-PPT"],"enzyme_classes":["2.7.8.-"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" magnesium ion binding"},{"category":"Function","description":" holo-[acyl-carrier-protein] synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, for other substituted phosphate groups"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" macromolecule biosynthetic process"}],"pfams":[{"name":"ACPS","identifier":"PF01648"}],"pathways":[],"gene_sequence":"ATGGTTAAAACGACTGAAGTAGTAAGCGAAGTTTCAAAGGTGGCAGGTGTAAGACCATGGGCAGGTATATTCGTTGTTGAAATTCAAGAGGATATACTCGCGGATGAGTTTACGTTCGAGGCATTAATGAGAACTTTGCCATTGGCGTCTCAAGCCAGAATCCTCAATAAAAAATCGTTTCACGATAGATGTTCAAATCTATGCAGCCAGCTGCTGCAGTTGTTTGGCTGCTCTATAGTAACGGGCTTAAATTTTCAAGAGCTGAAATTTGACAAGGGCAGCTTCGGTAAGCCATTCTTAGACAACAATCGTTTTCTTCCATTTAGCATGACCATCGGTGAACAATATGTAGCTATGTTCCTCGTAAAATGTGTAAGTACAGATGAATACCAGGATGTCGGAATTGATATCGCTTCTCCGTGCAATTATGGCGGGAGGGAAGAGTTGGAGCTATTTAAAGAAGTTTTTAGTGAAAGAGAATTTAACGGTTTACTGAAAGCGTCTGATCCATGCACAATATTTACTTACTTATGGTCCTTGAAGGAGTCGTATACAAAATTTACTGGAACTGGCCTTAACACAGACTTGTCACTAATAGATTTTGGCGCTATCAGCTTTTTTCCGGCTGAGGGAGCTTCTATGTGCATAACTCTGGATGAAGTTCCATTGATTTTCCATTCTCAATGGTTCAATAACGAAATTGTCACTATCTGTATGCCAAAGTCCATCAGTGATAAAATCAACACGAACAGACCAAAATTATATAATATCAGCTTATCTACGTTGATTGATTATTTCATCGAAAATGATGGTTTATAA","protein_sequence":"MVKTTEVVSEVSKVAGVRPWAGIFVVEIQEDILADEFTFEALMRTLPLASQARILNKKSFHDRCSNLCSQLLQLFGCSIVTGLNFQELKFDKGSFGKPFLDNNRFLPFSMTIGEQYVAMFLVKCVSTDEYQDVGIDIASPCNYGGREELELFKEVFSEREFNGLLKASDPCTIFTYLWSLKESYTKFTGTGLNTDLSLIDFGAISFFPAEGASMCITLDEVPLIFHSQWFNNEIVTICMPKSISDKINTNRPKLYNISLSTLIDYFIENDGL"}]}