{ "uniprot_canonical_ac": "Q04228-1", "uniprot_ac": "Q04228", "uniprot_id": "UBX2_YEAST", "mass": { "chemical_mass": 66761.0, "monoisotopic_mass": 66761.0 }, "refseq": { "ac": "NP_013699", "name": "Ubx2p", "summary": "", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_013699" }, "gene_names": [ { "name": "UBX2", "resource": "UniProtKB", "type": "recommended", "url": "https://www.uniprot.org/uniprot/Q04228", "id": "Q04228" }, { "name": "SEL1", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_013699", "id": "NP_013699" }, { "name": "SEL1", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/Q04228", "id": "Q04228" }, { "name": "UBX2", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_013699", "id": "NP_013699" }, { "name": "YM9571.05", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/Q04228", "id": "Q04228" } ], "protein_names": [ { "name": "UBX domain-containing protein 2", "resource": "UniProtKB", "type": "recommended", "url": "", "id": "Q04228" }, { "name": "Secretion lowering protein 1", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "Q04228" }, { "name": "Ubx2p", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_013699", "id": "NP_013699" } ], "function": [ { "annotation": "Integral endoplasmic reticulum membrane protein that coordinates the assembly of the ER-associated protein degradation (ERAD) machinery at the ER membrane. Mediates binding of CDC48 to the E3 ubiquitin ligases SSM4/DOA10 and HRD1, and to ERAD substrates. Component of the DOA10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains. ERAD-C substrates are ubiquitinated through DOA10 in conjunction with the E2 ubiquitin-conjugating enzymes UBC6 and UBC7-CUE1. Also a component of the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M). ERAD-L substrates are ubiquitinated through HRD1 in conjunction with the E2 ubiquitin-conjugating enzymes UBC1 and UBC7-CUE1. Ubiquitinated substrates are then removed to the cytosol via the action of the CDC48-NPL4-UFD1 ATPase complex and targeted to the proteasome.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228#function" }, { "database": "PubMed", "id": "15258615", "url": "https://glygen.org/publication/PubMed/15258615" }, { "database": "PubMed", "id": "16873066", "url": "https://glygen.org/publication/PubMed/16873066" }, { "database": "PubMed", "id": "16179952", "url": "https://glygen.org/publication/PubMed/16179952" }, { "database": "PubMed", "id": "16179953", "url": "https://glygen.org/publication/PubMed/16179953" } ] } ], "disease": [], "snv": [], "mutagenesis": [], "expression_tissue": [], "expression_disease": [], "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "common_name": "Yeast" } ], "gene": [ { "name": "UBX2", "url": "https://www.uniprot.org/uniprot/Q04228", "locus": { "chromosome": "XIII", "start_pos": 245903, "end_pos": 244149, "strand": "-", "evidence": [ { "database": "Ensembl Gene", "id": "YML013W", "url": "https://www.ensembl.org/id/YML013W" } ] } } ], "crossref": [ { "id": "cd14273", "url": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd14273", "database": "CDD", "categories": [ "Protein Classification" ] }, { "id": "854995", "url": "https://www.ncbi.nlm.nih.gov/gene/854995", "database": "GeneID", "categories": [ "Genome Annotation" ] }, { "id": "Q04228", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q04228*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "IPR001012", "url": "https://www.ebi.ac.uk/interpro/entry/IPR001012", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "sce:YML013W", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+sce:YML013W", "database": "KEGG Pathway", "categories": [ "Enzyme and Pathway" ] }, { "id": "VYAFVEC", "url": "https://omabrowser.org/oma/group/VYAFVEC/", "database": "OMA", "categories": [ "Protein Classification" ] }, { "id": "1989009at2759", "url": "http://www.orthodb.org/?query=1989009at2759", "database": "OrthoDB", "categories": [ "Protein Classification" ] }, { "id": "PTHR23322", "url": "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR23322", "database": "PANTHER", "categories": [ "Protein Classification" ] }, { "id": "PTHR23322:SF1", "url": "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR23322:SF1", "database": "PANTHER", "categories": [ "Protein Classification" ] }, { "id": "PF00789", "url": "http://pfam.xfam.org/family/PF00789", "database": "Pfam", "categories": [ "Protein Classification" ] }, { "id": "PF14555", "url": "http://pfam.xfam.org/family/PF14555", "database": "Pfam", "categories": [ "Protein Classification" ] }, { "id": "PR_Q04228", "url": "http://purl.obolibrary.org/obo/PR_Q04228", "database": "PRO", "categories": [ "Protein" ] }, { "id": "NP_013699", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_013699", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "S000004475", "url": "https://www.yeastgenome.org/locus/S000004475", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q04228-1", "url": "https://www.uniprot.org/uniprot/Q04228-1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "sequence": { "sequence": "MPVVNHEDSEFHLSHTEEDKLNEFQVITNFPPEDLPDVVRLLRNHGWQLEPALSRYFDGEWKGEPDQMGEPTQTSTPMAETLVPPALGPRPLLFTASLPVVRPLPANFRNDFRTIGLNGRSNTVWSMFESFSYDGNPFLFILLLIPRIINRLSATIFTFFCTLLSLHSISGGGNSGKPKISKVPKAPTRETHIPLAEILGDTKDKDAFCELKSFKPDISFNEALRIAKEEFKFMLLILVGDTYDTDTDTVDVNSKLLLEKILLNKKTLQYLRKIDNDLIIYLKCVHELEPWLVARQLGVRNTPEIFLIANVANKASHSETLPSQRLSILGKLKVNSLNRFLQSLTNVVEKYTPELVVNKTEMHELRMSREIKKLQEDAYKKSLEMDRIKAIEKEKSLKHAQDLKLNSTARQLKWLKACIDEIQPFETTGKQATLQFRTSSGKRFVKKFPSMTTLYQIYQSIGCHIYLAVYSSDPAEWSNALQDKIRQLSADDDMLCFKEGQLETATATTIEELGHIINNELTSFDLERGKLEFDFELVSPFPKYTVHPNEHMSVDQVPQLWPNGSLLVEALDEEDEEDEENEEQ", "length": 584, "header": "sp|Q04228-1|UBX2_YEAST Isoform 1 of UBX domain-containing protein 2 OS=Saccharomyces cerevisiae S288C OX=559292 GN=UBX2 PE=1 SV=1 CANONICAL=Q04228-1" }, "isoforms": [ { "isoform_ac": "Q04228-1", "url": "", "sequence": { "sequence": "MPVVNHEDSEFHLSHTEEDKLNEFQVITNFPPEDLPDVVRLLRNHGWQLEPALSRYFDGEWKGEPDQMGEPTQTSTPMAETLVPPALGPRPLLFTASLPVVRPLPANFRNDFRTIGLNGRSNTVWSMFESFSYDGNPFLFILLLIPRIINRLSATIFTFFCTLLSLHSISGGGNSGKPKISKVPKAPTRETHIPLAEILGDTKDKDAFCELKSFKPDISFNEALRIAKEEFKFMLLILVGDTYDTDTDTVDVNSKLLLEKILLNKKTLQYLRKIDNDLIIYLKCVHELEPWLVARQLGVRNTPEIFLIANVANKASHSETLPSQRLSILGKLKVNSLNRFLQSLTNVVEKYTPELVVNKTEMHELRMSREIKKLQEDAYKKSLEMDRIKAIEKEKSLKHAQDLKLNSTARQLKWLKACIDEIQPFETTGKQATLQFRTSSGKRFVKKFPSMTTLYQIYQSIGCHIYLAVYSSDPAEWSNALQDKIRQLSADDDMLCFKEGQLETATATTIEELGHIINNELTSFDLERGKLEFDFELVSPFPKYTVHPNEHMSVDQVPQLWPNGSLLVEALDEEDEEDEENEEQ", "length": 584, "header": "sp|Q04228-1|UBX2_YEAST Isoform 1 of UBX domain-containing protein 2 OS=Saccharomyces cerevisiae S288C OX=559292 GN=UBX2 PE=1 SV=1 CANONICAL=Q04228-1" }, "locus": { "chromosome": "XIII", "start_pos": 245900, "end_pos": 244149, "strand": "-", "evidence": [ { "database": "Ensembl Transcript", "id": "YML013W_mRNA", "url": "https://www.ensembl.org/id/YML013W_mRNA" }, { "database": "Ensembl Peptide", "id": "YML013W", "url": "https://www.ensembl.org/id/YML013W" } ] } } ], "glycosylation": [], "phosphorylation": [ { "start_pos": 318, "end_pos": 318, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "Q04228", "url": "https://www.yeastgenome.org/locus/Q04228" }, { "database": "iPTMnet", "id": "Q04228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q04228" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser318" }, { "start_pos": 427, "end_pos": 427, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q04228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q04228" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Thr427" } ], "glycation": [], "keywords": [], "publication": [ { "title": "Global analysis of protein localization in budding yeast.", "journal": "Nature", "date": "2003", "authors": "Weissman J.S., Carroll A.S., Howson R.W., Huh W.-K., O'Shea E.K., Falvo J.V., Gerke L.C.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "14562095", "url": "https://glygen.org/publication/PubMed/14562095" } ] }, { "title": "Global analysis of protein expression in yeast.", "journal": "Nature", "date": "2003", "authors": "Dephoure N., Weissman J.S., Howson R.W., Huh W.-K., O'Shea E.K., Belle A., Bower K., Ghaemmaghami S.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "14562106", "url": "https://glygen.org/publication/PubMed/14562106" } ] }, { "title": "Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin-dependent protein degradation.", "journal": "EMBO Rep.", "date": "2004", "authors": "Buchberger A., Richly H., Rumpf S., Schuberth C.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "15258615", "url": "https://glygen.org/publication/PubMed/15258615" } ] }, { "title": "Membrane-bound Ubx2 recruits Cdc48 to ubiquitin ligases and their substrates to ensure efficient ER-associated protein degradation.", "journal": "Nat. Cell Biol.", "date": "2005", "authors": "Buchberger A., Schuberth C.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "16179952", "url": "https://glygen.org/publication/PubMed/16179952" } ] }, { "title": "Ubx2 links the Cdc48 complex to ER-associated protein degradation.", "journal": "Nat. Cell Biol.", "date": "2005", "authors": "Walter J., Sommer T., Jarosch E., Volkwein C., Neuber O.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "16179953", "url": "https://glygen.org/publication/PubMed/16179953" } ] }, { "title": "Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins.", "journal": "Cell", "date": "2006", "authors": "Rapoport T.A., Carvalho P., Goder V.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "16873066", "url": "https://glygen.org/publication/PubMed/16873066" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "Q04228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q04228" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "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": "Q04228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q04228" } ], "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": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "24374639", "url": "https://glygen.org/publication/PubMed/24374639" } ] }, { "title": "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.", "journal": "Nature", "date": "1997", "authors": "Connor R., Gentles S., Pearson D., Bowman S., Hunt S., Barrell B.G., Skelton J., Brown D., Rice P., Odell C., Whitehead S., Badcock K., Chillingworth T., Churcher C.M., Dedman K., Devlin K., Hamlin N., Jagels K., Lye G., Moule S., Rajandream M.A., Walsh S.V.", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "reference": [ { "type": "PubMed", "id": "9169872", "url": "https://glygen.org/publication/PubMed/9169872" } ] } ], "pathway": [ { "id": "sce:YML013W", "name": "", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+sce:YML013W", "resource": "KEGG Pathway" } ], "orthologs": [], "go_annotation": { "categories": [ { "name": "Cellular Component", "total": 8, "go_terms": [ { "name": "mitochondrial outer membrane", "id": "GO:0005741", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005741", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "endoplasmic reticulum", "id": "GO:0005783", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005783", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "lipid droplet", "id": "GO:0005811", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005811", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "plasma membrane", "id": "GO:0005886", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005886", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "endoplasmic reticulum membrane", "id": "GO:0005789", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005789", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "Hrd1p ubiquitin ligase complex", "id": "GO:0000836", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0000836", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "Hrd1p ubiquitin ligase ERAD-L complex", "id": "GO:0000839", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0000839", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "Doa10p ubiquitin ligase complex", "id": "GO:0000837", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0000837", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" } ] }, { "name": "Molecular Function", "total": 2, "go_terms": [ { "name": "protein-macromolecule adaptor activity", "id": "GO:0030674", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030674", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "ubiquitin binding", "id": "GO:0043130", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0043130", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" } ] }, { "name": "Biological Process", "total": 6, "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": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "ubiquitin-dependent ERAD pathway", "id": "GO:0030433", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030433", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "mitochondria-associated ubiquitin-dependent protein catabolic process", "id": "GO:0072671", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0072671", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "mitochondrial protein processing", "id": "GO:0034982", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0034982", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "ER-associated misfolded protein catabolic process", "id": "GO:0071712", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0071712", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" }, { "name": "lipid droplet organization", "id": "GO:0034389", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0034389", "evidence": [ { "database": "UniProtKB", "id": "Q04228", "url": "https://www.uniprot.org/uniprot/Q04228" } ], "pmid": "" } ] } ] }, "pro_annotation": [], "site_annotation": [ { "start_pos": 358, "end_pos": 360, "annotation": "n_glycosylation_sequon" }, { "start_pos": 406, "end_pos": 408, "annotation": "n_glycosylation_sequon" }, { "start_pos": 563, "end_pos": 565, "annotation": 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