{"ymdb_id":"YMDB00904","created_at":"2011-05-29T19:03:17.000Z","updated_at":"2016-09-08T18:36:02.000Z","name":"Pectin","cas":"9000-69-5","state":"Solid","melting_point":"","description":"Pectin is a heterosaccharide derived from the cell wall of plants. Pectins vary in their chain lengths, complexity and the order of each of the monosaccharide units. The characteristic structure of pectin is a linear chain of alpha(1-\u003e4)linked D-galacturonic acid that forms the pectin-backbone, a homogalacturonan.","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"extracellular","synthesis_reference":"Gu, Qu-Ming; Nickol, Robert G.; Cheng, H. N. Enzyme-catalyzed modification of pectin. Polymer Preprints (American Chemical Society, Division of Polymer Chemistry) (2003), 44(2), 608-609.","chebi_id":"17309","hmdb_id":"HMDB03402","kegg_id":"C00714","pubchem_id":"854","cs_id":"25084799","foodb_id":null,"wikipedia_link":"Pectin","biocyc_id":"PECTIN","iupac":"(2S,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid","traditional_iupac":"β-D-galactopyranuronic acid","logp":"-2.61226468","pka":"11.309229286068723","alogps_solubility":"2.95e+02 g/l","alogps_logp":"-2.30","alogps_logs":"0.18","acceptor_count":"7","donor_count":"5","rotatable_bond_count":"1","polar_surface_area":"127.45000000000002","refractivity":"35.7908","polarizability":"16.369534945317536","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"-3.6863365702254773","pka_strongest_acidic":"3.207791058651709","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(+)-Xylose","2,3,4,5-Tetrahydroxypentanal","D-Lyxose","DL-Xylose","L-Lyxose","L(+)-Xylose","Lyxose","Pectin","Pectin sugar","Pectinose","Pentose","Trobicin"],"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"}],"growth_conditions":[],"references":[{"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":19840115,"citation":"Louw, C., Young, P. R., van Rensburg, P., Divol, B. (2010). \"Regulation of endo-polygalacturonase activity in Saccharomyces cerevisiae.\" FEMS Yeast Res 10:44-57."}],"proteins":[{"created_at":"2011-05-27T09:18:49.000Z","updated_at":"2011-07-22T17:54:40.000Z","name":"Polygalacturonase","uniprot_id":"P47180","uniprot_name":"PGLR_YEAST","enzyme":true,"transporter":false,"gene_name":"PGU1","num_residues":361,"molecular_weight":"37286.60156","theoretical_pi":"8.31","general_function":"Involved in polygalacturonase activity","specific_function":"Random hydrolysis of (1-\u003e4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans","reactions":[{"id":1476,"direction":null,"locations":"extracellular","altext":null,"export":true,"pw_reaction_id":null,"source":null}],"signal_regions":"1-18","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasmic","genbank_gene_id":"AB011818","genbank_protein_id":"2951783","gene_card_id":"PGU1","chromosome_location":"chromosome 10","locus":"YJR153W","synonyms":["PG","PGase SM","Pectinase"],"enzyme_classes":["3.2.1.15"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on glycosyl bonds"},{"category":"Function","description":" hydrolase activity, hydrolyzing O-glycosyl compounds"},{"category":"Function","description":" polygalacturonase 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":"Glyco_hydro_28","identifier":"PF00295"}],"pathways":[{"name":"Pentose and glucuronate interconversions","kegg_map_id":"00040"},{"name":"Starch and sucrose metabolism","kegg_map_id":"00500"}],"gene_sequence":"ATGATTTCTGCTAATTCATTACTTATTTCCACTTTGTGCGCTTTTGCGATCGCAACACCTTTGTCAAAAAGAGATTCCTGTACCCTAACAGGATCTTCTTTGTCTTCACTCTCAACCGTGAAAAAATGTAGCAGCATCGTTATTAAAGACTTAACTGTCCCAGCTGGACAGACTTTAGATTTAACTGGGTTAAGCAGTGGTACTACTGTTACGTTTGAAGGCACAACCACATTTCAGTACAAGGAATGGAGCGGCCCTTTAATTTCAATCTCAGGGTCTAAAATCAGCGTTGTTGGTGCTTCGGGACATACCATTGATGGTCAAGGAGCAAAATGGTGGGATGGCTTAGGTGATAGCGGTAAAGTCAAACCGAAGTTTGTAAAGTTGGCGTTGACGGGAACATCTAAGGTCACCGGATTGAATATTAAAAATGCTCCACACCAAGTCTTCAGCATCAATAAATGTTCAGATTTAACCATCAGCGACATAACAATTGATATCAGAGACGGTGATTCGGCTGGTGGTCATAATACGGATGGGTTTGATGTTGGTAGTTCTAGTAACGTCTTAATTCAAGGATGTACTGTTTATAATCAGGATGACTGTATTGCTGTGAATTCCGGTTCAACTATTAAATTTATGAACAACTACTGCTACAATGGCCATGGTATTTCTGTAGGTTCTGTTGGTGGCCGTTCTGATAATACAGTCAATGGTTTCTGGGCTGAAAATAACCATGTTATCAACTCTGACAACGGGTTGAGAATAAAAACCGTAGAAGGTGCGACAGGCACAGTCACTAATGTCAACTTTATCAGTAATAAAATTAGCGGCATAAAAAGTTATGGTATTGTTATCGAAGGCGATTATTTGAATAGTAAGACTACTGGAACTGCTACAGGTGGCGTTCCCATTTCGAATTTAGTAATGAAGGATATCACCGGGAGCGTGAACTCCACAGCGAAGAGGGTTAAAATTTTGGTGAAAAACGCTACTAACTGGCAATGGTCTGGGGTGTCAATTACCGGTGGTTCTTCCTATTCTGGATGTTCTGGAATCCCATCTGGATCTGGTGCAAGCTGTTAA","protein_sequence":"MISANSLLISTLCAFAIATPLSKRDSCTLTGSSLSSLSTVKKCSSIVIKDLTVPAGQTLDLTGLSSGTTVTFEGTTTFQYKEWSGPLISISGSKISVVGASGHTIDGQGAKWWDGLGDSGKVKPKFVKLALTGTSKVTGLNIKNAPHQVFSINKCSDLTISDITIDIRDGDSAGGHNTDGFDVGSSSNVLIQGCTVYNQDDCIAVNSGSTIKFMNNYCYNGHGISVGSVGGRSDNTVNGFWAENNHVINSDNGLRIKTVEGATGTVTNVNFISNKISGIKSYGIVIEGDYLNSKTTGTATGGVPISNLVMKDITGSVNSTAKRVKILVKNATNWQWSGVSITGGSSYSGCSGIPSGSGASC"}]}