{"ymdb_id":"YMDB00654","created_at":"2011-05-29T18:40:40.000Z","updated_at":"2016-09-08T18:35:44.000Z","name":"D-Arabinose","cas":"10323-20-3","state":"Solid","melting_point":"164-165 ºC ","description":"Arabinose is a five-carbon sugar (aldopentose). L-Arabinose is in fact more common than D-arabinose in nature and is found as a component of biopolymers such as hemicellulose and pectin.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"extracellular;cytoplasm","synthesis_reference":null,"chebi_id":"17108","hmdb_id":null,"kegg_id":"C00216","pubchem_id":"6902","cs_id":null,"foodb_id":null,"wikipedia_link":"Arabinose","biocyc_id":null,"iupac":"(2S,3R,4R)-2,3,4,5-tetrahydroxypentanal","traditional_iupac":"arabinose","logp":"-2.9380256209999995","pka":"13.420851692159264","alogps_solubility":"3.80e+02 g/l","alogps_logp":"-2.28","alogps_logs":"0.40","acceptor_count":"5","donor_count":"4","rotatable_bond_count":"4","polar_surface_area":"97.99000000000001","refractivity":"31.383099999999995","polarizability":"13.417572255354672","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.9744929158468105","pka_strongest_acidic":"12.332793333319174","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["D-Ara","D-Arabinose","Pentopyranose"],"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":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":10802179,"citation":"Hancock, R. D., Galpin, J. R., Viola, R. (2000). \"Biosynthesis of L-ascorbic acid (vitamin C) by Saccharomyces cerevisiae.\" FEMS Microbiol Lett 186:245-250."},{"pubmed_id":17097644,"citation":"Amako, K., Fujita, K., Shimohata, T. A., Hasegawa, E., Kishimoto, R., Goda, K. (2006). \"NAD+-specific D-arabinose dehydrogenase and its contribution to erythroascorbic acid production in Saccharomyces cerevisiae.\" FEBS Lett 580:6428-6434."}],"proteins":[{"created_at":"2011-05-24T20:01:41.000Z","updated_at":"2011-07-22T17:54:34.000Z","name":"D-arabinose dehydrogenase [NAD(P)+] heavy chain","uniprot_id":"P38115","uniprot_name":"ARA1_YEAST","enzyme":true,"transporter":false,"gene_name":"ARA1","num_residues":344,"molecular_weight":"38883.19922","theoretical_pi":"5.83","general_function":"Involved in oxidoreductase activity","specific_function":"Catalyzes the oxidation of D-arabinose, L-xylose, L- fucose and L-galactose in the presence of NADP+","reactions":[{"id":1433,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2292,"direction":"\u003e","locations":"Cytoplasm","altext":"D-arabinose + NAD(P)(+) = D-arabinono-1,4-lactone + NAD(P)H.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"Z36018","genbank_protein_id":"536474","gene_card_id":"ARA1","chromosome_location":"chromosome 2","locus":"YBR149W","synonyms":["AKR3C"],"enzyme_classes":["1.1.1.117"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" oxidation reduction"}],"pfams":[{"name":"Aldo_ket_red","identifier":"PF00248"}],"pathways":[],"gene_sequence":"ATGTCTTCTTCAGTAGCCTCAACCGAAAACATAGTCGAAAATATGTTGCATCCAAAGACTACAGAAATATACTTTTCACTCAACAATGGTGTTCGTATCCCAGCACTGGGTTTGGGGACAGCAAATCCTCACGAAAAGTTAGCTGAAACAAAACAAGCCGTAAAAGCTGCAATCAAAGCTGGATACAGGCACATTGATACTGCTTGGGCCTACGAGACAGAGCCATTCGTAGGTGAAGCCATCAAGGAGTTATTAGAAGATGGATCTATCAAAAGGGAGGATCTTTTCATAACCACAAAAGTGTGGCCGGTTCTATGGGACGAAGTGGACAGATCATTGAATGAATCTTTGAAAGCTTTAGGCTTGGAATACGTCGACTTGCTCTTGCAACATTGGCCGCTATGTTTTGAAAAGATTAAGGACCCTAAGGGGATCAGCGGACTGGTGAAGACTCCGGTTGATGATTCTGGAAAAACAATGTATGCTGCCGACGGTGACTATTTAGAAACTTACAAGCAATTGGAAAAAATTTACCTTGATCCTAACGATCATCGTGTGAGAGCCATTGGTGTCTCAAATTTTTCCATTGAGTATTTGGAACGTCTCATTAAGGAATGCAGAGTTAAGCCAACGGTGAACCAAGTGGAAACTCACCCTCACTTACCACAAATGGAACTAAGAAAGTTCTGCTTTATGCACGACATTCTGTTAACAGCATACTCACCATTAGGTTCCCATGGCGCACCAAACTTGAAAATCCCACTAGTGAAAAAGCTTGCCGAAAAGTACAATGTCACAGGAAATGACTTGCTAATTTCTTACCATATTAGACAAGGCACTATCGTAATTCCGAGATCCTTGAATCCAGTTAGGATTTCCTCGAGTATTGAATTCGCATCTTTGACAAAGGATGAATTACAAGAGTTGAACGACTTCGGTGAAAAATACCCAGTGAGATTCATCGATGAGCCATTTGCAGCCATCCTTCCAGAGTTTACTGGTAACGGACCAAACTTGGACAATTTAAAGTATTAA","protein_sequence":"MSSSVASTENIVENMLHPKTTEIYFSLNNGVRIPALGLGTANPHEKLAETKQAVKAAIKAGYRHIDTAWAYETEPFVGEAIKELLEDGSIKREDLFITTKVWPVLWDEVDRSLNESLKALGLEYVDLLLQHWPLCFEKIKDPKGISGLVKTPVDDSGKTMYAADGDYLETYKQLEKIYLDPNDHRVRAIGVSNFSIEYLERLIKECRVKPTVNQVETHPHLPQMELRKFCFMHDILLTAYSPLGSHGAPNLKIPLVKKLAEKYNVTGNDLLISYHIRQGTIVIPRSLNPVRISSSIEFASLTKDELQELNDFGEKYPVRFIDEPFAAILPEFTGNGPNLDNLKY"},{"created_at":"2011-05-24T20:02:44.000Z","updated_at":"2011-07-22T17:54:34.000Z","name":"D-arabinose 1-dehydrogenase","uniprot_id":"Q04212","uniprot_name":"ARA2_YEAST","enzyme":true,"transporter":false,"gene_name":"ARA2","num_residues":335,"molecular_weight":"38220.0","theoretical_pi":"5.28","general_function":"Involved in oxidoreductase activity","specific_function":"D-arabinose + NAD(+) = D-arabinono-1,4-lactone + NADH","reactions":[{"id":1432,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2294,"direction":"\u003e","locations":null,"altext":"D-arabinose + NAD(+) = D-arabinono-1,4-lactone + NADH.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AB237161","genbank_protein_id":"90991337","gene_card_id":"ARA2","chromosome_location":"chromosome 13","locus":"YMR041C","synonyms":["NAD(+)-specific D-arabinose dehydrogenase"],"enzyme_classes":["1.1.1.116"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" oxidation reduction"}],"pfams":[{"name":"Aldo_ket_red","identifier":"PF00248"}],"pathways":[],"gene_sequence":"ATGGTTAATGAAAAAGTGAATCCATTCGACTTAGCTTCGGTTTCTCCTTTAGTCTTAGGAGGTGCAATACTGAACCAGCAATATACAGATGAGCCAGAATCCATTCCACTGGAAGACATAATCAAATACGCATTTTCGCATGGTATCAATGCAATTGACACTTCTCCCTACTATGGCCCTAGTGAGGTTCTTTATGGTAGGGCACTGTCCAATTTAAGGAATGAATTTCCCAGAGACACTTATTTTATATGCACAAAGGTTGGGCGTATTGGTGCGGAAGAGTTTAACTATTCTAGAGATTTCGTGAGATTTAGTGTTCACAGATCGTGCGAAAGATTACACACTACATATCTCGATTTGGTGTACTTGCACGATGTCGAGTTTGTCAAATTTCCAGACATCTTAGAGGCATTAAAGGAATTGAGGACCTTGAAGAACAAAGGAGTTATCAAAAATTTTGGCATATCAGGCTACCCAATCGACTTTATCACCTGGCTTGCTGAGTACTGCTCTACCGAGGAAAGTGATATTGGGTCATTGGATGCAGTATTGTCCTATTGTAACTTGAACTTACAAAACAATAAGCTATTGAACTTTCGAGAAAGACTGCTACGCAATGCTAAACTGAAAATGGTTTGCAACGCATCAATCTTGAGCATGTCGCTACTAAGGTCACAGGAGACAAGACAGTTTCACCCGTGTTCTCATGAATTGAGAGAATGCGCATCTCAGGCTGCCAAATACTGTCAAGAACAAAATGTCGACTTAGCCGATTTGGCCACAAGATACGCGATTTCGGAATGGGTAGGAAAGGGACCCGTTGTTCTTGGAGTCAGTAGCATGGAAGAATTGAAACTTGCTCTGGATAATTACGAAATTGTGAAATCGAATGGCAACAGATTATCTTCTAAGGACGGACAACTAGTAGAATATATCCAAAAGAATATTTTTAAAGAACATTTTAATGAAGAGTGGTCTTCAGGTATTCCTCATCCAGAAATGATATAA","protein_sequence":"MVNEKVNPFDLASVSPLVLGGAILNQQYTDEPESIPLEDIIKYAFSHGINAIDTSPYYGPSEVLYGRALSNLRNEFPRDTYFICTKVGRIGAEEFNYSRDFVRFSVHRSCERLHTTYLDLVYLHDVEFVKFPDILEALKELRTLKNKGVIKNFGISGYPIDFITWLAEYCSTEESDIGSLDAVLSYCNLNLQNNKLLNFRERLLRNAKLKMVCNASILSMSLLRSQETRQFHPCSHELRECASQAAKYCQEQNVDLADLATRYAISEWVGKGPVVLGVSSMEELKLALDNYEIVKSNGNRLSSKDGQLVEYIQKNIFKEHFNEEWSSGIPHPEMI"}]}