{"ymdb_id":"YMDB00129","created_at":"2011-05-29T15:59:37.000Z","updated_at":"2016-09-08T18:35:04.000Z","name":"5-Methylthioribulose 1-phosphate","cas":"86316-83-8","state":"Solid","melting_point":"","description":"5-Methylthioribulose 1-phosphate is an intermediate in the methionine salvage pathway, which is found in a wide variety of organisms, including bacteria, protozoa, plants and mammals. [Biocyc PWY-4361]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Imker, Heidi J.; Fedorov, Alexander A.; Fedorov, Elena V.; Almo, Steven C.; Gerlt, John A.  Mechanistic Diversity in the RuBisCO Superfamily: The \"Enolase\" in the Methionine Salvage Pathway in Geobacillus kaustophilus.    Biochemistry  (2007),  46(13),  4","chebi_id":"28096","hmdb_id":"HMDB01299","kegg_id":"C04582","pubchem_id":"329","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":"CPD-1063","iupac":"{[(3R,4S)-3,4-dihydroxy-5-(methylsulfanyl)-2-oxopentyl]oxy}phosphonic acid","traditional_iupac":"methylthioribulose-1-phosphate","logp":"-1.2777918353333326","pka":"6.208835718373348","alogps_solubility":"1.93e+01 g/l","alogps_logp":"-0.43","alogps_logs":"-1.13","acceptor_count":"6","donor_count":"4","rotatable_bond_count":"7","polar_surface_area":"124.29000000000002","refractivity":"53.305800000000005","polarizability":"22.58689642828518","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.3648057294312927","pka_strongest_acidic":"1.1787298662051935","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["1-phospho-5-S-methylthioribulose","1-phosphomethylthioribulose","1PMT-ribulose","5-methylthio-2-ribulose-1-phosphate","5-Methylthio-5-deoxy-D-ribulose 1-phosphate","5-methylthio-5-deoxy-D-ribulose-1-phosphate","5-Methylthioribulose 1-phosphate","5-Methylthioribulose 1-phosphic acid","5-methylthioribulose-1-phosphate","5-S-methyl-1-O-phosphono-5-thio-D-ribulose","5-S-methyl-5-thio-D-erythro-pent-2-ulose 1-(dihydrogen phosphate)","5-S-methyl-5-thio-D-ribulose 1-(dihydrogen phosphate)","methylthioribulose-1-phosphate","MTRu-1-P","S-Methyl-5-thio-D-ribulose 1-phosphate"],"pathways":[{"name":"Cysteine and methionine metabolism","kegg_map_id":"00270"},{"name":"Methionine metabolism and salvage","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":18625006,"citation":"Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). \"A complete inventory of all enzymes in the eukaryotic methionine salvage pathway.\" FEBS J 275:4111-4120."}],"proteins":[{"created_at":"2011-05-24T20:34:56.000Z","updated_at":"2011-05-27T14:56:01.000Z","name":"Methylthioribulose-1-phosphate dehydratase","uniprot_id":"P47095","uniprot_name":"MTNB_YEAST","enzyme":true,"transporter":false,"gene_name":"MDE1","num_residues":244,"molecular_weight":"27426.59961","theoretical_pi":"6.59","general_function":"Involved in metal ion binding","specific_function":"Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P)","reactions":[{"id":2329,"direction":"\u003e","locations":"Cytoplasm","altext":"S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O.","export":false,"pw_reaction_id":null,"source":null},{"id":3793,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006312","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"AY692565","genbank_protein_id":"51012581","gene_card_id":"MDE1","chromosome_location":"chromosome 10","locus":"YJR024C","synonyms":["MTRu-1-P dehydratase"],"enzyme_classes":["4.2.1.109"],"go_classes":[{"category":"Component","description":" cytoplasm"},{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" binding"},{"category":"Process","description":" sulfur amino acid metabolic process"},{"category":"Process","description":" sulfur amino acid biosynthetic process"},{"category":"Process","description":" methionine biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" L-methionine biosynthetic process"},{"category":"Process","description":" L-methionine salvage"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"}],"pfams":[{"name":"Aldolase_II","identifier":"PF00596"}],"pathways":[{"name":"Cysteine and methionine metabolism","kegg_map_id":"00270"},{"name":"Methionine metabolism and salvage","kegg_map_id":null}],"gene_sequence":"ATGTCTTCACAAGATGTTCTGATACATTCAGATGATCCGTGCCATCCAGCAAATCTCATTTGCACGCTATGCAAGCAGTTTTTTCATAATAATTGGTGCACCGGAACTGGAGGTGGGATTTCAATAAAAGATCCTAACACGAATTATTATTATCTCGCCCCATCTGGGGTGCAGAAGGAGAAGATGATACCTGAGGATTTGTTTGTCATGGACGCTCAGACATTAGAGTATTTGCGCTCTCCCAAGCTTTACAAGCCAAGCGCATGTACTCCATTGTTCTTAGCGTGCTACCAAAAGAAAAATGCAGGTGCTATAATACATACACACTCCCAAAATGCTGTGATATGCTCCTTGCTATTTGGCGATGAGTTCAGGATTGCTAACATCGAACAAATCAAAGCAATTCCAAGCGGAAAGGTGGACCCTGTGACCAAGAAACCCATGGCGCTATCGTTTTTTGATACGCTGAAGATTCCCATCATTGAAAACATGGCGCATGAGGACGAGTTGATCGATGACTTGCACAAGACTTTTAAAGATTATCCAGACACATGCGCCGTAATTGTGAGGAGACATGGCATTTTTGTTTGGGGTCCGACAATCGATAAGGCCAAAATTTTCAACGAAGCCATCGATTATTTGATGGAGCTGGCCATAAAGATGTACCAAATGGGGATTCCTCCCGACTGTGGCATTGGCGAAGAGAAGAAGCATCTGAAGATGGCCAGTCCGTGA","protein_sequence":"MSSQDVLIHSDDPCHPANLICTLCKQFFHNNWCTGTGGGISIKDPNTNYYYLAPSGVQKEKMIPEDLFVMDAQTLEYLRSPKLYKPSACTPLFLACYQKKNAGAIIHTHSQNAVICSLLFGDEFRIANIEQIKAIPSGKVDPVTKKPMALSFFDTLKIPIIENMAHEDELIDDLHKTFKDYPDTCAVIVRRHGIFVWGPTIDKAKIFNEAIDYLMELAIKMYQMGIPPDCGIGEEKKHLKMASP"},{"created_at":"2011-05-24T21:10:24.000Z","updated_at":"2011-05-29T05:06:15.000Z","name":"Methylthioribose-1-phosphate isomerase","uniprot_id":"Q06489","uniprot_name":"MTNA_YEAST","enzyme":true,"transporter":false,"gene_name":"MRI1","num_residues":411,"molecular_weight":"45019.89844","theoretical_pi":"4.64","general_function":"Involved in cellular metabolic process","specific_function":"Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1- P)","reactions":[{"id":2364,"direction":"\u003e","locations":null,"altext":"S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":3794,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006313","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1W2W","cellular_location":null,"genbank_gene_id":"U40828","genbank_protein_id":"1066474","gene_card_id":"MRI1","chromosome_location":"chromosome 16","locus":"YPR118W","synonyms":["M1Pi","MTR-1-P isomerase","S-methyl-5-thioribose-1-phosphate isomerase"],"enzyme_classes":["5.3.1.23"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" Not Available"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular biosynthetic process"}],"pfams":[{"name":"IF-2B","identifier":"PF01008"}],"pathways":[{"name":"Cysteine and methionine metabolism","kegg_map_id":"00270"},{"name":"Methionine metabolism and salvage","kegg_map_id":null}],"gene_sequence":"ATGTCGTTGGAAGCCATCGTCTTTGATAGATCGGAGCCAGAAAATGTTTCGGTAAAGGTACTTGATCAATTACTTTTACCATATACTACTAAATACGTTCCAATTCACACAATTGATGATGGGTACTCAGTCATCAAAAGTATGCAGGTGAGAGGTGCCCCGGCAATTGCAATTGTGGGTTCGTTATCTGTTTTGACTGAGGTACAATTAATAAAACACAACCCAACTTCTGATGTTGCTACGCTGTATTCTTTAGTTAACTGGGAATCTACAAAAACAGTGCTAAATAAGAGGCTAGATTTCCTTTTGAGTAGTAGACCCACAGCCGTTAATTTATCAAATTCTCTTGTAGAGATAAAGAACATACTGAAATCCTCAAGTGACCTAAAGGCTTTTGACGGTAGTTTATATAATTACGTCTGTGAATTGATAGATGAGGATTTGGCGAATAACATGAAAATGGGTGATAATGGAGCTAAGTATTTGATTGACGTGTTACAAAAGGACGGTTTCAAGGACGAATTTGCCGTTCTGACGATTTGTAATACTGGATCCTTAGCAACCTCTGGATATGGCACGGCTTTAGGTGTTATCCGTTCTTTGTGGAAGGATTCACTTGCTAAAACCGACAAGGCAGACTCGGGATTGGACAATGAAAAATGCCCGAGGATGGGCCATGTCTTCCCACTGGAAACTAGACCTTATAATCAAGGGTCAAGGCTAACAGCATACGAGCTAGTTTATGATAAGATTCCATCAACTTTAATTACTGATAGTTCCATCGCGTATAGAATTAGAACTAGTCCAATTCCAATCAAAGCAGCATTTGTTGGAGCTGATAGAATTGTTCGTAATGGGGATACAGCAAATAAAATTGGTACTTTACAACTTGCTGTAATTTGTAAGCAGTTCGGAATTAAGTTTTTTGTAGTAGCTCCCAAAACAACTATCGATAATGTAACCGAAACTGGCGATGACATTATTGTGGAAGAACGTAACCCTGAGGAATTCAAGGTTGTTACTGGTACAGTAATTAATCCTGAAAATGGTTCCTTGATATTGAATGAGTCAGGAGAGCCAATCACTGGAAAGGTCGGTATTGCCCCTCTTGAAATCAATGTCTGGAATCCAGCCTTCGACATTACTCCACATGAGCTTATTGACGGAATTATCACAGAAGAAGGTGTATTTACCAAAAATTCCAGTGGTGAATTTCAACTGGAAAGCCTTTTCTAG","protein_sequence":"MSLEAIVFDRSEPENVSVKVLDQLLLPYTTKYVPIHTIDDGYSVIKSMQVRGAPAIAIVGSLSVLTEVQLIKHNPTSDVATLYSLVNWESTKTVLNKRLDFLLSSRPTAVNLSNSLVEIKNILKSSSDLKAFDGSLYNYVCELIDEDLANNMKMGDNGAKYLIDVLQKDGFKDEFAVLTICNTGSLATSGYGTALGVIRSLWKDSLAKTDKADSGLDNEKCPRMGHVFPLETRPYNQGSRLTAYELVYDKIPSTLITDSSIAYRIRTSPIPIKAAFVGADRIVRNGDTANKIGTLQLAVICKQFGIKFFVVAPKTTIDNVTETGDDIIVEERNPEEFKVVTGTVINPENGSLILNESGEPITGKVGIAPLEINVWNPAFDITPHELIDGIITEEGVFTKNSSGEFQLESLF"}]}