{"ymdb_id":"YMDB00362","created_at":"2011-05-29T18:09:47.000Z","updated_at":"2016-09-08T18:35:24.000Z","name":"Xylulose 5-phosphate","cas":"4212-65-1","state":"Solid","melting_point":"","description":"D-Xylulose 5-phosphate is an intermediate in the pentose phosphate pathway. The pentose phosphate pathway is an alternative way of oxidizing glucose and is important for the conversion of hexoses to pentoses. [Biocyc NONOXIPENT-PWY]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Shaeri, Jobin; Wohlgemuth, Roland; Woodley, John M.  Semiquantitative Process Screening for the Biocatalytic Synthesis of D-Xylulose-5-phosphate.    Organic Process Research \u0026 Development  (2006),  10(3),  605-610.","chebi_id":"16332","hmdb_id":"HMDB00868","kegg_id":"C00231","pubchem_id":"850","cs_id":"388330","foodb_id":null,"wikipedia_link":"Xylulose_5-phosphate","biocyc_id":"XYLULOSE-5-PHOSPHATE","iupac":"{[(2R,3S)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid","traditional_iupac":"ribulose-5-phosphate","logp":"-2.7602629813333333","pka":"6.504370847667953","alogps_solubility":"2.61e+01 g/l","alogps_logp":"-1.81","alogps_logs":"-0.95","acceptor_count":"7","donor_count":"5","rotatable_bond_count":"6","polar_surface_area":"144.52","refractivity":"42.472199999999994","polarizability":"18.05369731874536","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.3276267100529333","pka_strongest_acidic":"1.4785529591465414","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["D-xylulose 5-phosphate","D-xylulose 5-PO4","D-xylulose-5-P","D-xylulose-5-phosphate","Xu-5-P","Xylulose 5-phosphate","Xylulose 5-phosphic acid","xylulose-P","Xylulose-phosphate"],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"},{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"Methane metabolism","kegg_map_id":"00680"},{"name":"Riboneogenesis","kegg_map_id":null},{"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":10935926,"citation":"Vaseghi, S., Baumeister, A., Rizzi, M., Reuss, M. (1999). \"In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae.\" Metab Eng 1:128-140."},{"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."},{"pubmed_id":9032985,"citation":"Bar, J., Naumann, M., Reuter, R., Kopperschlager, G. (1996). \"Improved purification of ribulose 5-phosphate 3-epimerase from Saccharomyces cerevisiae and characterization of the enzyme.\" Bioseparation 6:233-241."}],"proteins":[{"created_at":"2011-05-26T17:22:26.000Z","updated_at":"2011-05-27T15:01:02.000Z","name":"Transketolase 2","uniprot_id":"P33315","uniprot_name":"TKT2_YEAST","enzyme":true,"transporter":false,"gene_name":"TKL2","num_residues":681,"molecular_weight":"75028.79688","theoretical_pi":"6.05","general_function":"Involved in catalytic activity","specific_function":"Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate","reactions":[{"id":2017,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2018,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2477,"direction":"\u003e","locations":"","altext":"Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14085,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006510","source":"Smpdb"},{"id":14086,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006512","source":"Smpdb"},{"id":14087,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006513","source":"Smpdb"},{"id":14088,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007089","source":"Smpdb"},{"id":14089,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007092","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X73532","genbank_protein_id":"313262","gene_card_id":"TKL2","chromosome_location":"chromosome 2","locus":"YBR117C","synonyms":["TK 2"],"enzyme_classes":["2.2.1.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring aldehyde or ketonic groups"},{"category":"Function","description":" transketolase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Transket_pyr","identifier":"PF02779"},{"name":"Transketolase_C","identifier":"PF02780"},{"name":"Transketolase_N","identifier":"PF00456"}],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"},{"name":"Riboneogenesis","kegg_map_id":null},{"name":"xylitol 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1","uniprot_id":"P23254","uniprot_name":"TKT1_YEAST","enzyme":true,"transporter":false,"gene_name":"TKL1","num_residues":680,"molecular_weight":"73805.0","theoretical_pi":"7.01","general_function":"Involved in catalytic activity","specific_function":"Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate","reactions":[{"id":2017,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2018,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2477,"direction":"\u003e","locations":"","altext":"Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14085,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006510","source":"Smpdb"},{"id":14086,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006512","source":"Smpdb"},{"id":14087,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006513","source":"Smpdb"},{"id":14088,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007089","source":"Smpdb"},{"id":14089,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007092","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1GPU","cellular_location":null,"genbank_gene_id":"U51033","genbank_protein_id":"1230682","gene_card_id":"TKL1","chromosome_location":"chromosome 16","locus":"YPR074C","synonyms":["TK 1"],"enzyme_classes":["2.2.1.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring aldehyde or ketonic groups"},{"category":"Function","description":" transketolase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Transket_pyr","identifier":"PF02779"},{"name":"Transketolase_C","identifier":"PF02780"},{"name":"Transketolase_N","identifier":"PF00456"}],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"},{"name":"Riboneogenesis","kegg_map_id":null},{"name":"xylitol 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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":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, alcohol group as acceptor"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"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":"2011-05-27T07:05:44.000Z","updated_at":"2011-05-27T15:01:27.000Z","name":"Ribulose-phosphate 3-epimerase","uniprot_id":"P46969","uniprot_name":"RPE_YEAST","enzyme":true,"transporter":false,"gene_name":"RPE1","num_residues":238,"molecular_weight":"25966.90039","theoretical_pi":"6.23","general_function":"Involved in catalytic activity","specific_function":"Involved in the protective response to oxidative stress","reactions":[{"id":1955,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2800,"direction":"\u003e","locations":"Cytoplasm","altext":"D-ribulose 5-phosphate = D-xylulose 5-phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14080,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006507","source":"Smpdb"},{"id":14081,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006509","source":"Smpdb"},{"id":14082,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007094","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"AY557858","genbank_protein_id":"45269607","gene_card_id":"RPE1","chromosome_location":"chromosome 10","locus":"YJL121C","synonyms":["Pentose-5-phosphate 3-epimerase","PPE","RPE"],"enzyme_classes":["5.1.3.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" isomerase activity"},{"category":"Function","description":" racemase and epimerase activity"},{"category":"Function","description":" racemase and epimerase activity, acting on carbohydrates and derivatives"},{"category":"Function","description":" ribulose-phosphate 3-epimerase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" primary metabolic process"},{"category":"Process","description":" carbohydrate metabolic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Ribul_P_3_epim","identifier":"PF00834"}],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"},{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"Riboneogenesis","kegg_map_id":null},{"name":"xylitol degradation","kegg_map_id":null}],"gene_sequence":"ATGGTCAAACCAATTATAGCTCCCAGTATCCTTGCTTCTGACTTCGCCAACTTGGGTTGCGAATGTCATAAGGTCATCAACGCCGGCGCAGATTGGTTACATATCGATGTCATGGACGGCCATTTTGTTCCAAACATTACTCTGGGCCAACCAATTGTTACCTCCCTACGTCGTTCTGTGCCACGCCCTGGCGATGCTAGCAACACAGAAAAGAAGCCCACTGCGTTCTTCGATTGTCACATGATGGTTGAAAATCCTGAAAAATGGGTCGACGATTTTGCTAAATGTGGTGCTGACCAATTTACGTTCCACTACGAGGCCACACAAGACCCTTTGCATTTAGTTAAGTTGATTAAGTCTAAGGGCATCAAAGCTGCATGCGCCATCAAACCTGGTACTTCTGTTGACGTTTTATTTGAACTAGCTCCTCATTTGGATATGGCTCTTGTTATGACTGTGGAACCTGGGTTTGGAGGCCAAAAATTCATGGAAGACATGATGCCAAAAGTGGAAACTTTGAGAGCCAAGTTCCCCCATTTGAATATCCAAGTCGATGGTGGTTTGGGCAAGGAGACCATCCCGAAAGCCGCCAAAGCCGGTGCCAACGTTATTGTCGCTGGTACCAGTGTTTTCACTGCAGCTGACCCGCACGATGTTATCTCCTTCATGAAAGAAGAAGTCTCGAAGGAATTGCGTTCTAGAGATTTGCTAGATTAG","protein_sequence":"MVKPIIAPSILASDFANLGCECHKVINAGADWLHIDVMDGHFVPNITLGQPIVTSLRRSVPRPGDASNTEKKPTAFFDCHMMVENPEKWVDDFAKCGADQFTFHYEATQDPLHLVKLIKSKGIKAACAIKPGTSVDVLFELAPHLDMALVMTVEPGFGGQKFMEDMMPKVETLRAKFPHLNIQVDGGLGKETIPKAAKAGANVIVAGTSVFTAADPHDVISFMKEEVSKELRSRDLLD"}]}