{"ymdb_id":"YMDB00700","created_at":"2011-05-29T18:44:36.000Z","updated_at":"2016-10-18T17:11:34.000Z","name":"dATP","cas":"1927-31-7","state":"Solid","melting_point":null,"description":"Deoxyadenosine triphosphate (dATP) is a nucleotide used in cells for DNA synthesis. DNA usually exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides having the bases: adenine, cytosine, guanine, and thymine. A nucleotide is a mono-, di-, or triphosphate deoxyribonucleoside; that is, a deoxyribose sugar is attached to one, two, or three phosphates. Chemical interaction of these nucleotides forms phosphodiester linkages, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides (bases) are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine, and cytosine pairs with guanine. [Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"16284","hmdb_id":"HMDB01532","kegg_id":"C00131","pubchem_id":"15993","cs_id":"23105280","foodb_id":null,"wikipedia_link":"Deoxyadenosine_triphosphate","biocyc_id":"DATP","iupac":"({[({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid","traditional_iupac":"dATP","logp":"-4.910784043786679","pka":"2.5152845517576545","alogps_solubility":"3.83e+00 g/l","alogps_logp":"-0.66","alogps_logs":"-2.11","acceptor_count":"13","donor_count":"6","rotatable_bond_count":"8","polar_surface_area":"258.9","refractivity":"94.30359999999997","polarizability":"38.05574342232156","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"4.030117344716746","pka_strongest_acidic":"0.8954169891075989","bioavailability":"0","number_of_rings":"3","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["2-deoxyadenosine 5-triphosphate","2'-Deoxy-5'-ATP","2'-Deoxy-ATP","2'-Deoxyadenosine 5'-triphosphate","2'-deoxyadenosine triphosphate","dATP","Deoxy-ATP","deoxyadenosine 5-triphosphate","Deoxyadenosine 5'-triphosphate","deoxyadenosine triphosphate","deoxyadenosine-triphosphate","DTP"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"purine nucleotides de novo biosynthesis","kegg_map_id":null}],"growth_conditions":[{"growth_media":"YEPD medium","concentration":"44.0","concentration_units":"\u0026#181;M","error":"0.0"}],"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":17227840,"citation":"Chabes, A., Stillman, B. (2007). \"Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae.\" Proc Natl Acad Sci U S A 104:1183-1188."},{"pubmed_id":12581528,"citation":"Chabes, A., Georgieva, B., Domkin, V., Zhao, X., Rothstein, R., Thelander, L. (2003). \"Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase.\" Cell 112:391-401."},{"pubmed_id":8837737,"citation":"Prieto, S., Bouillaud, F., Rial, E. (1996). \"The nature and regulation of the ATP-induced anion permeability in Saccharomyces cerevisiae mitochondria.\" Arch Biochem Biophys 334:43-49."},{"pubmed_id":8634337,"citation":"Coda-Zabetta, F., Boam, D. S. (1996). \"Distinct effects of ATP on transcription complex formation and initiation in a yeast in vitro transcription system.\" Biochim Biophys Acta 1306:194-202."},{"pubmed_id":7929110,"citation":"Muller, E. G. (1994). \"Deoxyribonucleotides are maintained at normal levels in a yeast thioredoxin mutant defective in DNA synthesis.\" J Biol Chem 269:24466-24471."},{"pubmed_id":14573610,"citation":"Koc, A., Wheeler, L. J., Mathews, C. K., Merrill, G. F. (2004). \"Hydroxyurea arrests DNA replication by a mechanism that preserves basal dNTP pools.\" J Biol Chem 279:223-230."}],"proteins":[{"created_at":"2011-05-26T16:57:01.000Z","updated_at":"2011-05-27T15:01:01.000Z","name":"Nucleoside diphosphate kinase","uniprot_id":"P36010","uniprot_name":"NDK_YEAST","enzyme":true,"transporter":false,"gene_name":"YNK1","num_residues":153,"molecular_weight":"17166.59961","theoretical_pi":"9.05","general_function":"Involved in nucleoside diphosphate kinase activity","specific_function":"Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage","reactions":[{"id":1786,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1787,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1788,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1789,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1790,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1791,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1792,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1793,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1794,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2454,"direction":"\u003e","locations":"Cytoplasm. Mitochondrion intermembrane space.","altext":"ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Mitochondrion intermembrane space.","genbank_gene_id":"AY558263","genbank_protein_id":"45270416","gene_card_id":"YNK1","chromosome_location":"chromosome 11","locus":"YKL067W","synonyms":["NDK","NDP kinase"],"enzyme_classes":["2.7.4.6"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"category":"Function","description":" nucleoside diphosphate kinase activity"},{"category":"Process","description":" GTP biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" purine nucleoside triphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" purine ribonucleoside triphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" CTP biosynthetic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleoside triphosphate biosynthetic process"},{"category":"Process","description":" purine nucleotide biosynthetic process"},{"category":"Process","description":" pyrimidine ribonucleoside triphosphate biosynthetic process"},{"category":"Process","description":" UTP biosynthetic process"}],"pfams":[{"name":"NDK","identifier":"PF00334"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGTCTAGTCAAACAGAAAGAACTTTTATTGCGGTAAAACCAGATGGTGTCCAGAGGGGCTTAGTATCTCAAATTCTATCTCGTTTTGAAAAAAAAGGTTACAAACTAGTTGCTATTAAATTAGTTAAAGCGGATGATAAATTACTAGAGCAACATTACGCAGAGCATGTTGGTAAACCATTTTTCCCAAAGATGGTATCCTTTATGAAGTCTGGTCCCATTTTGGCCACGGTCTGGGAGGGAAAAGATGTGGTTAGACAAGGAAGAACTATTCTTGGTGCTACTAATCCTTTGGGCAGTGCACCAGGTACCATTAGAGGTGATTTCGGTATTGACCTAGGCAGAAACGTCTGTCACGGCAGTGATTCTGTTGATAGCGCTGAACGTGAAATCAATTTGTGGTTTAAGAAGGAAGAGTTAGTTGATTGGGAATCTAATCAAGCTAAGTGGATTTATGAATGA","protein_sequence":"MSSQTERTFIAVKPDGVQRGLVSQILSRFEKKGYKLVAIKLVKADDKLLEQHYAEHVGKPFFPKMVSFMKSGPILATVWEGKDVVRQGRTILGATNPLGSAPGTIRGDFGIDLGRNVCHGSDSVDSAEREINLWFKKEELVDWESNQAKWIYE"},{"created_at":"2011-05-27T00:02:34.000Z","updated_at":"2011-07-22T17:54:35.000Z","name":"Guanylate kinase","uniprot_id":"P15454","uniprot_name":"KGUA_YEAST","enzyme":true,"transporter":false,"gene_name":"GUK1","num_residues":187,"molecular_weight":"20637.19922","theoretical_pi":"7.34","general_function":"Involved in protein binding","specific_function":"Essential for recycling GMP and indirectly, cGMP","reactions":[{"id":1443,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1622,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1623,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2618,"direction":"\u003e","locations":null,"altext":"ATP + GMP = ADP + GDP.","export":false,"pw_reaction_id":null,"source":null},{"id":14313,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006812","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1EX7","cellular_location":null,"genbank_gene_id":"L04683","genbank_protein_id":"171625","gene_card_id":"GUK1","chromosome_location":"chromosome 4","locus":"YDR454C","synonyms":["GMP kinase"],"enzyme_classes":["2.7.4.8"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" guanylate kinase 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, phosphate group as acceptor"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" purine nucleotide metabolic process"}],"pfams":[{"name":"Guanylate_kin","identifier":"PF00625"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"purine nucleotides de novo biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGTCCCGTCCTATCGTAATTTCTGGCCCAAGTGGTACAGGTAAATCTACACTGTTGAAGAAATTGTTCGCTGAATACCCAGATTCTTTCGGGTTTAGTGTTTCATCCACTACTAGAACCCCAAGAGCTGGCGAAGTAAACGGTAAGGACTATAACTTTGTCTCCGTAGATGAATTCAAATCTATGATTAAGAACAATGAATTCATTGAATGGGCGCAATTCTCCGGTAACTACTATGGTAGTACTGTCGCTTCCGTCAAACAAGTCAGTAAATCTGGTAAGACTTGTATTTTAGATATTGATATGCAGGGTGTCAAATCTGTCAAGGCTATCCCAGAGTTAAATGCCAGGTTTTTGTTTATTGCTCCACCATCGGTCGAGGATTTGAAAAAAAGATTAGAAGGTAGAGGTACGGAGACCGAAGAATCCATCAACAAGAGGTTAAGCGCCGCTCAAGCTGAATTGGCATATGCTGAGACAGGTGCCCATGACAAAGTTATTGTCAATGATGATTTGGACAAGGCCTACAAGGAATTGAAGGATTTTATCTTTGCAGAAAAATGA","protein_sequence":"MSRPIVISGPSGTGKSTLLKKLFAEYPDSFGFSVSSTTRTPRAGEVNGKDYNFVSVDEFKSMIKNNEFIEWAQFSGNYYGSTVASVKQVSKSGKTCILDIDMQGVKSVKAIPELNARFLFIAPPSVEDLKKRLEGRGTETEESINKRLSAAQAELAYAETGAHDKVIVNDDLDKAYKELKDFIFAEK"},{"created_at":"2011-05-27T03:51:12.000Z","updated_at":"2011-05-27T15:01:21.000Z","name":"Thioredoxin-2","uniprot_id":"P22803","uniprot_name":"TRX2_YEAST","enzyme":true,"transporter":false,"gene_name":"TRX2","num_residues":104,"molecular_weight":"11203.7998","theoretical_pi":"4.54","general_function":"Involved in electron carrier activity","specific_function":"Participates as a hydrogen donor in redox reactions through the reversible oxidation of its active center dithiol to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. It is involved in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding, sulfur metabolism, and redox homeostasis. Thioredoxin-dependent enzymes include phosphoadenosine-phosphosulfate reductase MET16, alkyl- hydroperoxide reductase DOT5, thioredoxin peroxidases TSA1 and TSA2, alkyl hydroperoxide reductase AHP1, and peroxiredoxin HYR1. Thioredoxin is also involved in protection against reducing stress. As part of the LMA1 complex, it is involved in the facilitation of vesicle fusion such as homotypic vacuole and ER- derived COPII vesicle fusion with the Golgi. This activity does not require the redox mechanism. Through its capacity to inactivate the stress response transcription factor YAP1 and its regulator the hydroperoxide stress sensor HYR1, it is involved in feedback regulation of stress response gene expression upon oxidative stress","reactions":[{"id":1949,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1950,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1951,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1952,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein. Nucleus","genbank_gene_id":"AY557817","genbank_protein_id":"45269525","gene_card_id":"TRX2","chromosome_location":"chromosome 7","locus":"YGR209C","synonyms":["Thioredoxin II","TR-II","Thioredoxin-1"],"enzyme_classes":[],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" electron carrier activity"},{"category":"Function","description":" oxidoreductase activity, acting on a sulfur group of donors"},{"category":"Function","description":" disulfide oxidoreductase activity"},{"category":"Function","description":" protein disulfide oxidoreductase activity"},{"category":"Process","description":" glycerol ether metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" cellular process"},{"category":"Process","description":" cellular homeostasis"},{"category":"Process","description":" cell redox homeostasis"},{"category":"Process","description":" organic ether metabolic process"}],"pfams":[{"name":"Thioredoxin","identifier":"PF00085"}],"pathways":[],"gene_sequence":"ATGGTCACTCAATTAAAATCCGCTTCTGAATACGACAGTGCTTTAGCATCTGGCGACAAGTTAGTCGTTGTTGACTTTTTTGCCACATGGTGTGGGCCATGTAAAATGATTGCACCAATGATTGAAAAGTTTGCAGAACAATATTCTGACGCTGCTTTTTACAAGTTGGATGTTGATGAAGTCTCAGATGTTGCTCAAAAAGCTGAAGTTTCTTCCATGCCTACCCTAATCTTCTACAAGGGCGGTAAGGAGGTTACCAGAGTCGTCGGTGCCAACCCAGCTGCTATCAAGCAAGCTATTGCTTCCAACGTATAG","protein_sequence":"MVTQLKSASEYDSALASGDKLVVVDFFATWCGPCKMIAPMIEKFAEQYSDAAFYKLDVDEVSDVAQKAEVSSMPTLIFYKGGKEVTRVVGANPAAIKQAIASNV"},{"created_at":"2011-05-27T03:51:46.000Z","updated_at":"2011-05-27T15:01:21.000Z","name":"Thioredoxin-1","uniprot_id":"P22217","uniprot_name":"TRX1_YEAST","enzyme":true,"transporter":false,"gene_name":"TRX1","num_residues":103,"molecular_weight":"11234.90039","theoretical_pi":"4.54","general_function":"Involved in electron carrier activity","specific_function":"Participates as a hydrogen donor in redox reactions through the reversible oxidation of its active center dithiol to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. It is involved in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding, sulfur metabolism, and redox homeostasis. Thioredoxin-dependent enzymes include phosphoadenosine-phosphosulfate reductase MET16, alkyl- hydroperoxide reductase DOT5, thioredoxin peroxidases TSA1 and TSA2, alkyl hydroperoxide reductase AHP1, and peroxiredoxin HYR1. Thioredoxin is also involved in protection against reducing stress. As part of the LMA1 complex, it is involved in the facilitation of vesicle fusion such as homotypic vacuole and ER- derived COPII vesicle fusion with the Golgi. This activity does not require the redox mechanism","reactions":[{"id":1949,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1950,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1951,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1952,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein. Nucleus","genbank_gene_id":"AY558203","genbank_protein_id":"45270296","gene_card_id":"TRX1","chromosome_location":"chromosome 12","locus":"YLR043C","synonyms":["Thioredoxin I","TR-I","Thioredoxin-2"],"enzyme_classes":[],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" electron carrier activity"},{"category":"Function","description":" oxidoreductase activity, acting on a sulfur group of donors"},{"category":"Function","description":" disulfide oxidoreductase activity"},{"category":"Function","description":" protein disulfide oxidoreductase activity"},{"category":"Process","description":" glycerol ether metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" cellular process"},{"category":"Process","description":" cellular homeostasis"},{"category":"Process","description":" cell redox homeostasis"},{"category":"Process","description":" organic ether metabolic process"}],"pfams":[{"name":"Thioredoxin","identifier":"PF00085"}],"pathways":[],"gene_sequence":"ATGGTTACTCAATTCAAAACTGCCAGCGAATTCGACTCTGCAATTGCTCAAGACAAGCTAGTTGTCGTAGATTTCTACGCCACTTGGTGCGGTCCATGTAAAATGATTGCTCCAATGATTGAAAAATTCTCTGAACAATACCCACAAGCTGATTTCTATAAATTGGATGTCGATGAATTGGGTGATGTTGCACAAAAGAATGAAGTTTCCGCTATGCCAACTTTGCTTCTATTCAAGAACGGTAAGGAAGTTGCAAAGGTTGTTGGTGCCAACCCAGCGGCTATTAAGCAAGCCATTGCTGCTAATGCTTAA","protein_sequence":"MVTQFKTASEFDSAIAQDKLVVVDFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIAANA"}]}