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"database": "PDB", "categories": [ "3D Structure" ] }, { "id": "PF00227", "url": "http://pfam.xfam.org/family/PF00227", "database": "Pfam", "categories": [ "Protein Classification" ] }, { "id": "PR_P25451", "url": "http://purl.obolibrary.org/obo/PR_P25451", "database": "PRO", "categories": [ "Protein" ] }, { "id": "NP_011020", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_011020", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "S000000896", "url": "https://www.yeastgenome.org/locus/S000000896", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P25451-1", "url": "https://www.uniprot.org/uniprot/P25451-1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "sequence": { "sequence": "MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYLKMRQD", "length": 205, "header": "sp|P25451-1|PSB3_YEAST Isoform 1 of Proteasome subunit beta type-3 OS=Saccharomyces cerevisiae S288C OX=559292 GN=PUP3 PE=1 SV=1 CANONICAL=P25451-1" }, "isoforms": [ { "isoform_ac": "P25451-1", "url": "", "sequence": { "sequence": "MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYLKMRQD", "length": 205, "header": "sp|P25451-1|PSB3_YEAST Isoform 1 of Proteasome subunit beta type-3 OS=Saccharomyces cerevisiae S288C OX=559292 GN=PUP3 PE=1 SV=1 CANONICAL=P25451-1" }, "locus": { "chromosome": "V", "start_pos": 349346, "end_pos": 348732, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "YER094C_mRNA", "url": "https://www.ensembl.org/id/YER094C_mRNA" }, { "database": "Ensembl Peptide", "id": "YER094C", "url": "https://www.ensembl.org/id/YER094C" } ] } } ], "glycosylation": [], "phosphorylation": [ { "start_pos": 2, "end_pos": 2, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Ser2" }, { "start_pos": 31, "end_pos": 31, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" }, { "database": "SGD", "id": "P25451", "url": "https://www.yeastgenome.org/locus/P25451" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser31" }, { "start_pos": 33, "end_pos": 33, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "P25451", "url": "https://www.yeastgenome.org/locus/P25451" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser33" } ], "glycation": [], "keywords": [], "publication": [ { "title": "A gated channel into the proteasome core particle.", "journal": "Nat. Struct. Biol.", "date": "2000", "authors": "Huber R., Finley D., Moroder L., Koehler A., Bajorek M., Glickman M.H., Groll M., Rubin D.M.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "11062564", "url": "https://glygen.org/publication/PubMed/11062564" } ] }, { "title": "Structural basis for the activation of 20S proteasomes by 11S regulators.", "journal": "Nature", "date": "2000", "authors": "Whitby F.G., Yao Y., Hill C.P., Wang C.C., Knowlton J.R., Kramer L., Masters E.I.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "11081519", "url": "https://glygen.org/publication/PubMed/11081519" } ] }, { "title": "Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene RAD51.", "journal": "Mol. Cell. Biol.", "date": "1992", "authors": "Aker M., Mortimer R.K., Basile G.M.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "1620128", "url": "https://glygen.org/publication/PubMed/1620128" } ] }, { "title": "Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome.", "journal": "Structure", "date": "2006", "authors": "Ploegh H.L., Ovaa H., Berkers C.R., Groll M.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "16531229", "url": "https://glygen.org/publication/PubMed/16531229" } ] }, { "title": "Crystal structures of salinosporamide A (NPI-0052) and B (NPI-0047) in complex with the 20S proteasome reveal important consequences of beta-lactone ring opening and a mechanism for irreversible binding.", "journal": "J. Am. Chem. Soc.", "date": "2006", "authors": "Huber R., Groll M., Potts B.C.M.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "16608349", "url": "https://glygen.org/publication/PubMed/16608349" } ] }, { "title": "TMC-95-based inhibitor design provides evidence for the catalytic versatility of the proteasome.", "journal": "Chem. Biol.", "date": "2006", "authors": "Moroder L., Kaiser M., Goetz M., Groll M., Weyher E.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "16793518", "url": "https://glygen.org/publication/PubMed/16793518" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" }, { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening.", "journal": "Mol. Cell", "date": "2010", "authors": "Sadre-Bazzaz Kianoush, Whitby Frank G, Robinson Howard, Formosa Tim, Hill Christopher P", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "20227375", "url": "https://glygen.org/publication/PubMed/20227375" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Sites of ubiquitin attachment in Saccharomyces cerevisiae.", "journal": "Proteomics", "date": "2012", "authors": "Eng J.K., Fields S., Lo R.S., Starita L.M., von Haller P.D.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "22106047", "url": "https://glygen.org/publication/PubMed/22106047" } ] }, { "title": "Near-atomic resolution structural model of the yeast 26S proteasome.", "journal": "Proc. Natl. Acad. Sci. U.S.A.", "date": "2012", "authors": "Villa E., Baumeister W., Beck F., Pfeifer G., Plitzko J.M., Sakata E., Schweitzer A., Forster F., Bohn S., Nickell S., Unverdorben P.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "22927375", "url": "https://glygen.org/publication/PubMed/22927375" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P25451", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25451" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "journal": "G3 (Bethesda)", "date": "2014", "authors": "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "24374639", "url": "https://glygen.org/publication/PubMed/24374639" } ] }, { "title": "Structure of 20S proteasome from yeast at 2.4-A resolution.", "journal": "Nature", "date": "1997", "authors": "Groll M, Ditzel L, L\u00f6we J, Stock D, Bochtler M, Bartunik H D, Huber R", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "9087403", "url": "https://glygen.org/publication/PubMed/9087403" } ] }, { "title": "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "journal": "Nature", "date": "1997", "authors": "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "reference": [ { "type": "PubMed", "id": "9169868", "url": "https://glygen.org/publication/PubMed/9169868" } ] } ], "pathway": [ { "id": "sce:YER094C", "name": "", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+sce:YER094C", "resource": "KEGG Pathway" } ], "orthologs": [ { "uniprot_canonical_ac": "P49720-1", "protein_name": "Proteasome subunit beta type-3", "gene_name": "PSMB3", "tax_id": 9606, "organism": "Homo sapiens", "sequence": { "sequence": "MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTLKARMD", "length": 205 }, "evidence": [ { "id": "P25451", "url": "https://omabrowser.org/oma/group/P25451/", "database": "OMA" } ], "common_name": "Human" }, { "uniprot_canonical_ac": "Q9R1P1-1", "protein_name": "Proteasome subunit beta type-3", "gene_name": "Psmb3", "tax_id": 10090, "organism": "Mus musculus", "sequence": { "sequence": "MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCSEQMYGMCESLWEPNMDPEHLFETISQAMLNAVDRDAVSGMGVIVHVIEKDKITTRTLKARMD", "length": 205 }, "evidence": [ { "id": "P25451", "url": "https://omabrowser.org/oma/group/P25451/", "database": "OMA" } ], "common_name": "Mouse" }, { "uniprot_canonical_ac": "Q9XYN7-1", "protein_name": "Proteasome subunit beta type-3", "gene_name": "Prosbeta3", "tax_id": 7227, "organism": "Drosophila melanogaster", "sequence": { "sequence": "MSILAYNGGCVVAMRGKDCVAIATDHRFGIQAQTISTDFKKVFHIGPRMFLGLTGLQTDILTVRDRLMFRKNLYETRENREMCPKPFSAMMSSFLYEHRFGPYFIEPVVAGLDPKTMEPFICNMDLIGCPNAPDDFVVAGTCAEQLYGMCETLWKPDLEPDQLFEVIAQSIVNAFDRDAMSGWGATVYIIEKDKITERTLKTRMD", "length": 205 }, "evidence": [ { "id": "P25451", "url": "https://omabrowser.org/oma/group/P25451/", "database": "OMA" } ], "common_name": "Fruit fly" } ], "go_annotation": { "categories": [ { "name": "Cellular Component", "total": 4, "go_terms": [ { "name": "proteasome core complex, beta-subunit complex", "id": "GO:0019774", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0019774", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" }, { "name": "nucleus", "id": "GO:0005634", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005634", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" }, { "name": "cytoplasm", "id": "GO:0005737", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005737", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" }, { "name": "proteasome complex", "id": "GO:0000502", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0000502", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" } ] }, { "name": "Biological Process", "total": 3, "go_terms": [ { "name": "proteasome-mediated ubiquitin-dependent protein catabolic process", "id": "GO:0043161", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0043161", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" }, { "name": "proteasomal protein catabolic process", "id": "GO:0010498", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0010498", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" }, { "name": "proteasomal ubiquitin-independent protein catabolic process", "id": "GO:0010499", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0010499", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" } ] }, { "name": "Molecular Function", "total": 1, "go_terms": [ { "name": "endopeptidase activator activity", "id": "GO:0061133", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0061133", "evidence": [ { "database": "UniProtKB", "id": "P25451", "url": "https://www.uniprot.org/uniprot/P25451" } ], "pmid": "" } ] } ] }, "pro_annotation": [], "site_annotation": [], "ptm_annotation": [], "interactions": [], "reactions": [], "reaction_participants": [], "reaction_enzymes": [], "biomarkers": [], "synthesized_glycans": [], "cluster_types": [ { "name": "homologset.oma", "label": "OMA Homologs" } ], "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": 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