{"ymdb_id":"YMDB00161","created_at":"2011-05-29T16:02:40.000Z","updated_at":"2016-09-08T18:35:07.000Z","name":"D-Xylulose","cas":"551-84-8","state":"Liquid","melting_point":"15 oC","description":"Xylulose is a ketopentose, a monosaccharide containing five carbon atoms, and including a ketone functional group. In nature, it occurs in both the L- and D-enantiomers. [Wikipedia]\n","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Takeuchi, Sonoko; Tonouchi, Naoto; Yokozeki, Kenzo.  Production of xylitol or D-xylulose by fermentation of glucose with Gluconobacter, Acetobacter, and Frateuria.    Eur. Pat. Appl.  (2000),     10 pp. ","chebi_id":"17140","hmdb_id":"HMDB01644","kegg_id":"C00310","pubchem_id":"619","cs_id":null,"foodb_id":null,"wikipedia_link":"Xylulose","biocyc_id":"D-XYLULOSE","iupac":"(3S,4R)-1,3,4,5-tetrahydroxypentan-2-one","traditional_iupac":"D-xylulose","logp":"-2.63669695","pka":"13.995534588386644","alogps_solubility":"6.78e+02 g/l","alogps_logp":"-2.16","alogps_logs":"0.65","acceptor_count":"5","donor_count":"4","rotatable_bond_count":"4","polar_surface_area":"97.99","refractivity":"31.5993","polarizability":"13.525589692915348","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.9797457089641277","pka_strongest_acidic":"10.569923731220491","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["D-threo-Pentulose","D-Xylulose","Xylulose"],"pathways":[{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"xylitol degradation","kegg_map_id":null}],"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":16348083,"citation":"Senac, T., Hahn-Hagerdal, B. (1990). \"Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells.\" Appl Environ Microbiol 56:120-126."}],"proteins":[{"created_at":"2011-05-27T00:58:15.000Z","updated_at":"2011-05-27T15:01:14.000Z","name":"Xylulose kinase","uniprot_id":"P42826","uniprot_name":"XKS1_YEAST","enzyme":true,"transporter":false,"gene_name":"XKS1","num_residues":600,"molecular_weight":"68320.29688","theoretical_pi":"6.82","general_function":"Involved in phosphotransferase activity, alcohol group as acceptor","specific_function":"ATP + D-xylulose = ADP + D-xylulose 5- phosphate","reactions":[{"id":2052,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2626,"direction":"\u003e","locations":"Cytoplasm","altext":"ATP + D-xylulose = ADP + D-xylulose 5-phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14079,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006506","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"Z72979","genbank_protein_id":"1323345","gene_card_id":"XKS1","chromosome_location":"chromosome 7","locus":"YGR194C","synonyms":["Xylulokinase"],"enzyme_classes":["2.7.1.17"],"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":"Function","description":" phosphotransferase activity, alcohol group as acceptor"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" primary metabolic process"},{"category":"Process","description":" carbohydrate metabolic process"}],"pfams":[{"name":"FGGY_C","identifier":"PF02782"},{"name":"FGGY_N","identifier":"PF00370"}],"pathways":[{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"xylitol degradation","kegg_map_id":null}],"gene_sequence":"ATGTTGTGTTCAGTAATTCAGAGACAGACAAGAGAGGTTTCCAACACAATGTCTTTAGACTCATACTATCTTGGGTTTGATCTTTCGACCCAACAACTGAAATGTCTCGCCATTAACCAGGACCTAAAAATTGTCCATTCAGAAACAGTGGAATTTGAAAAGGATCTTCCGCATTATCACACAAAGAAGGGTGTCTATATACACGGCGACACTATCGAATGTCCCGTAGCCATGTGGTTAGAGGCTCTAGATCTGGTTCTCTCGAAATATCGCGAGGCTAAATTTCCATTGAACAAAGTTATGGCCGTCTCAGGGTCCTGCCAGCAGCACGGGTCTGTCTACTGGTCCTCCCAAGCCGAATCTCTGTTAGAGCAATTGAATAAGAAACCGGAAAAAGATTTATTGCACTACGTGAGCTCTGTAGCATTTGCAAGGCAAACCGCCCCCAATTGGCAAGACCACAGTACTGCAAAGCAATGTCAAGAGTTTGAAGAGTGCATAGGTGGGCCTGAAAAAATGGCTCAATTAACAGGGTCCAGAGCCCATTTTAGATTTACTGGTCCTCAAATTCTGAAAATTGCACAATTAGAACCAGAAGCTTACGAAAAAACAAAGACCATTTCTTTAGTGTCTAATTTTTTGACTTCTATCTTAGTGGGCCATCTTGTTGAATTAGAGGAGGCAGATGCCTGTGGTATGAACCTTTATGATATACGTGAAAGAAAATTCAGTGATGAGCTACTACATCTAATTGATAGTTCTTCTAAGGATAAAACTATCAGACAAAAATTAATGAGAGCACCCATGAAAAATTTGATAGCGGGTACCATCTGTAAATATTTTATTGAGAAGTACGGTTTCAATACAAACTGCAAGGTCTCTCCCATGACTGGGGATAATTTAGCCACTATATGTTCTTTACCCCTGCGGAAGAATGACGTTCTCGTTTCCCTAGGAACAAGTACTACAGTTCTTCTGGTCACCGATAAGTATCACCCCTCTCCGAACTATCATCTTTTCATTCATCCAACTCTGCCAAACCATTATATGGGTATGATTTGTTATTGTAATGGTTCTTTGGCAAGGGAGAGGATAAGAGACGAGTTAAACAAAGAACGGGAAAATAATTATGAGAAGACTAACGATTGGACTCTTTTTAATCAAGCTGTGCTAGATGACTCAGAAAGTAGTGAAAATGAATTAGGTGTATATTTTCCTCTGGGGGAGATCGTTCCTAGCGTAAAAGCCATAAACAAAAGGGTTATCTTCAATCCAAAAACGGGTATGATTGAAAGAGAGGTGGCCAAGTTCAAAGACAAGAGGCACGATGCCAAAAATATTGTAGAATCACAGGCTTTAAGTTGCAGGGTAAGAATATCTCCCCTGCTTTCGGATTCAAACGCAAGCTCACAACAGAGACTGAACGAAGATACAATCGTGAAGTTTGATTACGATGAATCTCCGCTGCGGGACTACCTAAATAAAAGGCCAGAAAGGACTTTTTTTGTAGGTGGGGCTTCTAAAAACGATGCTATTGTGAAGAAGTTTGCTCAAGTCATTGGTGCTACAAAGGGTAATTTTAGGCTAGAAACACCAAACTCATGTGCCCTTGGTGGTTGTTATAAGGCCATGTGGTCATTGTTATATGACTCTAATAAAATTGCAGTTCCTTTTGATAAATTTCTGAATGACAATTTTCCATGGCATGTAATGGAAAGCATATCCGATGTGGATAATGAAAATTGGGATCGCTATAATTCCAAGATTGTCCCCTTAAGCGAACTGGAAAAGACTCTCATCTAA","protein_sequence":"MLCSVIQRQTREVSNTMSLDSYYLGFDLSTQQLKCLAINQDLKIVHSETVEFEKDLPHYHTKKGVYIHGDTIECPVAMWLEALDLVLSKYREAKFPLNKVMAVSGSCQQHGSVYWSSQAESLLEQLNKKPEKDLLHYVSSVAFARQTAPNWQDHSTAKQCQEFEECIGGPEKMAQLTGSRAHFRFTGPQILKIAQLEPEAYEKTKTISLVSNFLTSILVGHLVELEEADACGMNLYDIRERKFSDELLHLIDSSSKDKTIRQKLMRAPMKNLIAGTICKYFIEKYGFNTNCKVSPMTGDNLATICSLPLRKNDVLVSLGTSTTVLLVTDKYHPSPNYHLFIHPTLPNHYMGMICYCNGSLARERIRDELNKERENNYEKTNDWTLFNQAVLDDSESSENELGVYFPLGEIVPSVKAINKRVIFNPKTGMIEREVAKFKDKRHDAKNIVESQALSCRVRISPLLSDSNASSQQRLNEDTIVKFDYDESPLRDYLNKRPERTFFVGGASKNDAIVKKFAQVIGATKGNFRLETPNSCALGGCYKAMWSLLYDSNKIAVPFDKFLNDNFPWHVMESISDVDNENWDRYNSKIVPLSELEKTLI"},{"created_at":"2011-05-27T01:37:20.000Z","updated_at":"2011-05-27T15:01:15.000Z","name":"D-xylulose reductase","uniprot_id":"Q07993","uniprot_name":"XYL2_YEAST","enzyme":true,"transporter":false,"gene_name":"XYL2","num_residues":356,"molecular_weight":"38600.10156","theoretical_pi":"6.06","general_function":"Involved in zinc ion binding","specific_function":"Xylitol + NAD(+) = D-xylulose + NADH","reactions":[{"id":2050,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2632,"direction":"\u003e","locations":null,"altext":"Xylitol + NAD(+) = D-xylulose + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":14077,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006504","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"Z73242","genbank_protein_id":"1360424","gene_card_id":"XYL2","chromosome_location":"chromosome 12","locus":"YLR070C","synonyms":["Xylitol dehydrogenase","XDH"],"enzyme_classes":["1.1.1.9"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" transition metal ion binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" zinc ion binding"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" oxidation reduction"}],"pfams":[{"name":"ADH_N","identifier":"PF08240"},{"name":"ADH_zinc_N","identifier":"PF00107"}],"pathways":[{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"xylitol degradation","kegg_map_id":null}],"gene_sequence":"ATGACTGACTTAACTACACAAGAAGCTATTGTTCTAGAGCGACCTGGTAAAATCACCCTAACTAATGTCAGCATCCCAAAGATTTCAGATCCTAACGAAGTAATCATCCAGATCAAGGCGACAGGAATATGCGGGTCAGATATCCATTACTATACCCATGGAAGAATAGCCAATTACGTGGTAGAATCACCAATGGTGCTGGGACATGAATCATCAGGAATAGTGGCCCTCATAGGTGAGAACGTCAAGACACTTAAAGTAGGAGATAGGGTGGCACTTGAGCCCGGAATACCTGACAGGTTTTCACCGGAGATGAAAGAGGGCAGATACAACCTGGACCCCAATTTAAAATTTGCTGCGACACCTCCCTTTGATGGGACCTTGACAAAGTATTATAAGACCATGAAAGATTTCGTCTATAAACTTCCTGATGATGTGTCATTCGAGGAAGGAGCACTAATAGAGCCATTATCAGTGGCAATCCATGCTAATAAATTAGCAAAGATCAAGTTTGGAGCCCGTTGCGTCGTCTTTGGAGCTGGGCCCATAGGTTTGCTAGCCGGGAAAGTAGCCAGTGTCTTTGGTGCTGCAGATGTTGTTTTTGTAGATCTATTAGAAAACAAGCTGGAAACGGCTAGGCAGTTTGGTGCCACCCACATCGTCAACTCAGGTGATCTCCCACATGGCGTTACTGTAGATAGTGTTATAAAAAAAGCAATCGGCAAGAAAGGTGCTGACGTTGTGTTTGAATGTTCTGGTGCAGAGCCTTGCGTTCGAGCAGGCATCGAAGTCTGTAAGGCAGGTGGAACGATCGTTCAAGTTGGAATGGGACAAGAGGAAATACAATTTCCCATCTCGATCATTCCAACAAAAGAACTGACATTCCAAGGCTGTTTCCGATACTGTCAAGGTGATTATAGTGACTCCATCGAGCTAGTCTCTAGCAGAAAACTCTCGCTTAAACCATTCATTACACATCGCTATAGCTTTAAGGATGCTGTCGAGGCATTCGAAGAAACAAGCCACCACCCGTTAAATAATATCAAGACGATCATTGAGGGCCCGGAATGA","protein_sequence":"MTDLTTQEAIVLERPGKITLTNVSIPKISDPNEVIIQIKATGICGSDIHYYTHGRIANYVVESPMVLGHESSGIVALIGENVKTLKVGDRVALEPGIPDRFSPEMKEGRYNLDPNLKFAATPPFDGTLTKYYKTMKDFVYKLPDDVSFEEGALIEPLSVAIHANKLAKIKFGARCVVFGAGPIGLLAGKVASVFGAADVVFVDLLENKLETARQFGATHIVNSGDLPHGVTVDSVIKKAIGKKGADVVFECSGAEPCVRAGIEVCKAGGTIVQVGMGQEEIQFPISIIPTKELTFQGCFRYCQGDYSDSIELVSSRKLSLKPFITHRYSFKDAVEAFEETSHHPLNNIKTIIEGPE"}]}