{"ymdb_id":"YMDB00779","created_at":"2011-05-29T18:52:24.000Z","updated_at":"2016-09-08T18:35:53.000Z","name":"aldehydo-D-Xylose","cas":"58-86-6","state":"Solid","melting_point":"90.5 oC","description":"Xylose is a five-carbon sugar (aldopentose). Only the D-isomers are known to occur naturally. D-xylose is the precursor to hemicellulose in plants. Aldehydo-D-xylose is the acyclic form of D-xylose.","experimental_water_solubility":"555 mg/mL [MERCK INDEX (1996)]","experimental_logp_hydrophobicity":null,"location":"extracellular;cytoplasm","synthesis_reference":"Lavarack, B. P.; Griffin, G.; Rodman, D.  Optimizing the autohydrolysis of bagasse to extract D-xylose.    Proceedings of the Conference of the Australian Society of Sugar Cane Technologists  (1999),  21st  394-400. ","chebi_id":"15936","hmdb_id":"HMDB00098","kegg_id":"C00181","pubchem_id":"644160","cs_id":null,"foodb_id":null,"wikipedia_link":"Xylose","biocyc_id":"XYLOSE","iupac":"(3R,4S,5R)-oxane-2,3,4,5-tetrol","traditional_iupac":"d-xylose","logp":"-2.302204276","pka":"12.786263151759016","alogps_solubility":"1.22e+03 g/l","alogps_logp":"-2.57","alogps_logs":"0.91","acceptor_count":"5","donor_count":"4","rotatable_bond_count":"0","polar_surface_area":"90.15","refractivity":"29.9609","polarizability":"13.432709748510788","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-3.5265718350182684","pka_strongest_acidic":"11.310624247742409","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(+)-Xylose","(D)-Xylose","aldehydo-D-xylose","D-(+)-xylose","D-Xyl","D-xylo-pentose","d-Xylose","Pentose","wood sugar","Xylo-pfan","Xylomed","Xylose","Xylose, d-","Xyloside"],"pathways":[{"name":"Amino sugar and nucleotide sugar metabolism","kegg_map_id":"00520"},{"name":"Starch and sucrose metabolism","kegg_map_id":"00500"},{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"xylitol degradation","kegg_map_id":null}],"growth_conditions":[],"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":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":"2011-05-27T01:58:22.000Z","updated_at":"2011-07-22T17:54:34.000Z","name":"NADPH-dependent aldose reductase GRE3","uniprot_id":"P38715","uniprot_name":"GRE3_YEAST","enzyme":true,"transporter":false,"gene_name":"GRE3","num_residues":327,"molecular_weight":"37118.5","theoretical_pi":"7.09","general_function":"Involved in oxidoreductase activity","specific_function":"Reduces the cytotoxic compound methylglyoxal (MG) to (R)-lactaldehyde similar to GRE2. MG is synthesized via a bypath of glycolysis from dihydroxyacetone phosphate and is believed to play a role in cell cycle regulation and stress adaptation. In pentose-fermenting yeasts, aldose reductase catalyzes the reduction of xylose into xylitol. The purified enzyme catalyzes this reaction, but the inability of S.cerevisiae to grow on xylose as sole carbon source indicates that the physiological function is more likely methylglyoxal reduction","reactions":[{"id":1292,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1325,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1436,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1702,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2051,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2650,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"Alditol + NAD(P)(+) = aldose + NAD(P)H.","export":false,"pw_reaction_id":null,"source":null},{"id":2651,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"(R)-lactaldehyde + NADP(+) = methylglyoxal + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":14078,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006505","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"U00059","genbank_protein_id":"529125","gene_card_id":"GRE3","chromosome_location":"chromosome 8","locus":"YHR104W","synonyms":["Genes de respuesta a estres protein 3","NADPH-dependent aldo-keto reductase GRE3","NADPH-dependent methylglyoxal reductase GRE3","Xylose reductase"],"enzyme_classes":["1.1.1.21","1.1.1.-"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Aldo_ket_red","identifier":"PF00248"}],"pathways":[{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"Fructose and mannose metabolism","kegg_map_id":"00051"},{"name":"Galactose metabolism","kegg_map_id":"00052"},{"name":"Glycerolipid metabolism","kegg_map_id":"00561"},{"name":"Pyruvate metabolism","kegg_map_id":"00620"},{"name":"xylitol degradation","kegg_map_id":null}],"gene_sequence":"ATGTCTTCACTGGTTACTCTTAATAACGGTCTGAAAATGCCCCTAGTCGGCTTAGGGTGCTGGAAAATTGACAAAAAAGTCTGTGCGAATCAAATTTATGAAGCTATCAAATTAGGCTACCGTTTATTCGATGGTGCTTGCGACTACGGCAACGAAAAGGAAGTTGGTGAAGGTATCAGGAAAGCCATCTCCGAAGGTCTTGTTTCTAGAAAGGATATATTTGTTGTTTCAAAGTTATGGAACAATTTTCACCATCCTGATCATGTAAAATTAGCTTTAAAGAAGACCTTAAGCGATATGGGACTTGATTATTTAGACCTGTATTATATTCACTTCCCAATCGCCTTCAAATATGTTCCATTTGAAGAGAAATACCCTCCAGGATTCTATACGGGCGCAGATGACGAGAAGAAAGGTCACATCACCGAAGCACATGTACCAATCATAGATACGTACCGGGCTCTGGAAGAATGTGTTGATGAAGGCTTGATTAAGTCTATTGGTGTTTCCAACTTTCAGGGAAGCTTGATTCAAGATTTATTACGTGGTTGTAGAATCAAGCCCGTGGCTTTGCAAATTGAACACCATCCTTATTTGACTCAAGAACACCTAGTTGAGTTTTGTAAATTACACGATATCCAAGTAGTTGCTTACTCCTCCTTCGGTCCTCAATCATTCATTGAGATGGACTTACAGTTGGCAAAAACCACGCCAACTCTGTTCGAGAATGATGTAATCAAGAAGGTCTCACAAAACCATCCAGGCAGTACCACTTCCCAAGTATTGCTTAGATGGGCAACTCAGAGAGGCATTGCCGTCATTCCAAAATCTTCCAAGAAGGAAAGGTTACTTGGCAACCTAGAAATCGAAAAAAAGTTCACTTTAACGGAGCAAGAATTGAAGGATATTTCTGCACTAAATGCCAACATCAGATTTAATGATCCATGGACCTGGTTGGATGGTAAATTCCCCACTTTTGCCTGA","protein_sequence":"MSSLVTLNNGLKMPLVGLGCWKIDKKVCANQIYEAIKLGYRLFDGACDYGNEKEVGEGIRKAISEGLVSRKDIFVVSKLWNNFHHPDHVKLALKKTLSDMGLDYLDLYYIHFPIAFKYVPFEEKYPPGFYTGADDEKKGHITEAHVPIIDTYRALEECVDEGLIKSIGVSNFQGSLIQDLLRGCRIKPVALQIEHHPYLTQEHLVEFCKLHDIQVVAYSSFGPQSFIEMDLQLAKTTPTLFENDVIKKVSQNHPGSTTSQVLLRWATQRGIAVIPKSSKKERLLGNLEIEKKFTLTEQELKDISALNANIRFNDPWTWLDGKFPTFA"}]}