{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v01/MSV000078983/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Brian Raught"],"instrument_platform":["LTQ Orbitrap Velos"],"species":["Homo Sapiens (ncbitaxon:9606)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=5c514d0f39f94aa6aab8c8fc56aa3907"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["356"],"ptm_modification":["MOD:00425 - \"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\"","MOD:00400 - \"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\"","MOD:00428 - \"A protein modification that effectively replaces two hydrogen atoms with two hydroxyl groups.\""],"data_protocol":[""],"pubmed_abstract":["RAD6 is a ubiquitin E2 protein with roles in a number of different biological processes. Here, using affinity purification coupled with mass spectrometry, we identify a number of new RAD6 binding partners, including the poorly characterized ubiquitin E3 ligases KCMF1 (potassium channel modulatory factor 1) and UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4), a protein that can bind N-end rule substrates, and which was recently linked to lysosome-mediated degradation and autophagy. NMR, combined with in vivo and in vitro interaction mapping, demonstrate that the KCMF1 C terminus binds directly to RAD6, whereas N-terminal domains interact with UBR4 and other intracellular vesicle- and mitochondria-associated proteins. KCMF1 and RAD6 colocalize at late endosomes and lysosomes, and cells disrupted for KCMF1 or RAD6 function display defects in late endosome vesicle dynamics. Notably, we also find that two different RAD6A point mutants (R7W and R11Q) found in X-linked intellectual disability (XLID) patients specifically lose the interaction with KCMF1 and UBR4, but not with other previously identified RAD6 interactors. We propose that RAD6-KCMF1-UBR4 represents a unique new E2-E3 complex that targets unknown N-end rule substrates for lysosome-mediated degradation, and that disruption of this complex via RAD6A mutations could negatively affect neuronal function in XLID patients."],"pubmed_title":["KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation."],"pubmed_authors":["Hong Jenny H JH, Kaustov Lilia L, Coyaud Etienne E, Srikumar Tharan T, Wan Janet J, Arrowsmith Cheryl C, Raught Brian B"],"description_synonyms":["biochemical pathways, projections, single-organism catabolic process, multicellular organismal catabolic process, Bru, IPP2A2, l(3)Ca, Raw, PNT-P1, mCRY, DmelCG17077, alpha-Spe, 26S protease, d-titin, EY3-1, protein, Pnt, Autolysosome, Mitochondrial Contractions, alpha-Spc, 5730420M11Rik, l(3)04276, large multicatalytic protease, protein polypeptide chains, png, DmelCG1915, 1, cellular degradation, Analysis, hhr6a, D-ets-2, 3520, multicatalytic endopeptidase complex, protein aggregate, Ket, WMS, alpha-spec, Pnt-P1, Mass Spectrum Analysis, Svc, SET, kus, High Mobility Protein 20, Analyses, TAF-I, catabolism, Iprit, RBAF600, Ubiquitin-related 1, proteins, purification, ket, alpha-spectrin, DmelCG4299, isolation and purification, Ligase, APF-1, IGAAD, set, A930005E13Rik, CG14648, DmelCG10574, papilla, mustard gas, polyhedral organelle, tripeptidyl-peptidase II activity, biotransformation, p600, associated, AHUS2, GPHYSD2, TRA2.10, mKIAA0462, multicatalytic proteinase, ZZZ1, SGS, Potassium channel modulatory factor, phapii, Growl, 6.3.2.-, MRXSN, titin, lamina, flanges, StF-IT-1, Gm1666, late, D-Ets-2, ets94F, 0123/09, 0020/01, threonine endopeptidase activity, CEP52, Spectrum Analysis, L-ornithine carboxy-lyase activity, results, Autolysosomes, ACMICD, Spectroscopy, alphaSpec, CFU-MC, bis(2-chloroethyl)sulfane, l(1)G0108, shelf, membrane-enclosed vesicle, secretion, prosome, Mutant, spectrin, Mutant Protein, tricorn proteinase, Ubiq, Ubiquitin, Mitochondrial, pntP2, Rad6, RAD6, D930005K06Rik, breakdown, Pointed-P1, HLA-DR-associated protein II, DI-2, Debt91, shelves, I-2Dm, Ets94F, Human Ubiquitin, Spectrometry, MASS, alpha, CG4299, MIC10, projection, ridge, I-2PP1, TLX, ptd, PntP2, CG1915, TAF-IBETA, PCMF, Patient, X-linked intellectual disability, PntP1, i6, multicatalytic proteinase (complex), E(E2F)3D, CG18242, tricorn protease, PNTP2, TAF-Ibeta, i2pp2a, alkaline protease, PNTP1, Specbeta, CG18245, FIGC, 0998/12, anon-EST:fe2E2, Lysosome, l(3)alpha-Spec, FGF-induced in gastric cancer, lamellae, ETS2, Kcmf1, Ets2, alpha-Spect, CG2013, number, FBN, Gene, Synthetases, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, Spectrum Analyses, Yperite, Mbh1, protein-containing complex, SLS, Sls, process of organ, cellular catabolism, DEBT91, PHAPII, Human, ingensin, lamella, RAD6A, DMPOINT1A, pntegfr, 0608/07, N28143, B-spec, PSO8, polypeptide chain, isolation, ECTOL1, HEL-S-66, betaspec, klo, Gene Products, Mass, Mitochondrion, HMG-20, alpha-Sp, Del(8)44H, Titin, Mustard gas, Crry, CG1977, 1'-thiobis(2-chloroethane), anon-CREST, CFU-Mast, Mass Spectroscopy, l(3)j1D7, 1700094M07Rik, 1810009A16Rik, pointed-RC, ubc2, breakdown of chemical, AFCP, Receptosome, ligand, Contraction, ipp2a2, anon-WO0118547.126, dre3, colony forming unit mast cell, 2pp2a, TPP, ridges, CG18857, growl, EK3-2, CG10574, OCTD, anon-EST:fe1B3, bis(2-chloroethyl) sulphide, Lost, l(3)07825, l(3)dre8, lens neutral proteinase, 40S ribosomal protein S27a, Pmcf, 2PP2A, SPEC8, taf-ibeta, Clients, ubiquitin, KZ, dSET, dSet, l(3)rL182, CG17077, DmelCG14648, CG5870, protein tagging activity, laminae, Mcp, MCP, membrane-bounded vesicle, l(3)j1B7, l(3)dre3, sulfur mustard, Spec-beta, cellular breakdown, HHR6A, Ets, alpha-Spectrin, Dhr6, degradation, 1-chloro-2-[(2-chloroethyl)thio]ethane, 3A9, Zubr1, protein complex, DmelCG1977, Proteins, igaad, Rbed1, l(3)62Ca, function, i168, SpeC, Client, L-ornithine carboxy-lyase (putrescine-forming), Endosome, Cell, nev, group, kettin, Contractions, Mutant., DmelCG2013, Ubiquitin A-52 residue ribosomal protein fusion product 1, MS, native protein, natural protein, I-2PP2A, Ubiquitin-related 2, MRXS30, Protein, Dm I-2, I2PP2A, Synthetase, betaSpec, MFS1, rad6a, ATP-Dependent Proteolysis Factor 1, Receptosomes, alphaSp, b-Spec, pnt-P1, UBC2, pnt-P2, flange, Mass Spectrum Analyses, l(3)s118306, WMS2, organ process, breakdown of molecule, D-titin, covalent modifier, Mass Spectrum, DmelCG5870, l(1)G0074, Col4a-1, l(1)G0198, biodegradation, ensemble, FCP-B, b spectrin, Senfgas, D-Titin, ZZ-type zinc finger-containing protein 1, ZUBR1, beta, sam, sal, Protein Gene Products, Mitochondrial Contraction, Gene Proteins, processes, dSET/TAF-Ibeta, breakdown of substance, Ets58AB, 2610030F17Rik, mitochondria, CT41299, 60S ribosomal protein L40, beta-spec, l(3)62Bd, ligase, SSKS, cardinality, l(3)S002001, alfa-Spec, Ubiquitin-related, AA407739, BcDNA:RE56673, Gm1032, Spec, POINT, proteasome endopeptidase complex, CG8705"],"pubmed_abstract_synonyms":["projections, biochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, ER-Phagy, PNT-P1, DmelCG17077, EY3-1, protein, Pnt, Autolysosome, Mitochondrial Contractions, Mutations, protein polypeptide chains, png, cellular degradation, Analysis, hhr6a, D-ets-2, 3520, protein aggregate, Pnt-P1, Mass Spectrum Analysis, High Mobility Protein 20, Analyses, catabolism, Moods, RBAF600, Ubiquitin-related 1, proteins, purification, isolation and purification, Ligase, APF-1, A930005E13Rik, ER Phagy, papilla, Nucleophagy, biotransformation, p600, associated, mKIAA0462, ZZZ1, Potassium channel modulatory factor, 6.3.2.-, MRXSN, lamina, flanges, Gm1666, late, D-Ets-2, ets94F, 0123/09, Ribophagy, CEP52, Spectrum Analysis, Autolysosomes, Spectroscopy, Reticulophagy, shelf, membrane-enclosed vesicle, Autophagocytosis, Cellular, secretion, END, Ubiq, Ubiquitin, Mitochondrial, pntP2, Rad6, RAD6, D930005K06Rik, breakdown, Pointed-P1, Debt91, Autophagy, shelves, Ets94F, Human Ubiquitin, Spectrometry, projection, ridge, ptd, PntP2, PCMF, Patient, X-linked intellectual disability, PntP1, E(E2F)3D, PNTP2, PNTP1, PVC, FIGC, 0998/12, Lysosome, FGF-induced in gastric cancer, lamellae, ETS2, Kcmf1, Ets2, CG2013, number, Gene, Lipophagy, Synthetases, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, Spectrum Analyses, protein-containing complex, process of organ, cellular catabolism, DEBT91, Human, lamella, RAD6A, DMPOINT1A, pntegfr, 0608/07, Client., N28143, PSO8, polypeptide chain, isolation, Gene Products, Mass, Mitochondrion, Cellular Autophagy, HMG-20, Mood, Mass Spectroscopy, 1700094M07Rik, 1810009A16Rik, pointed-RC, ubc2, breakdown of chemical, Receptosome, ligand, Contraction, ridges, EK3-2, l(3)07825, 40S ribosomal protein S27a, Pmcf, Clients, ubiquitin, CG17077, protein tagging activity, laminae, membrane-bounded vesicle, HHT1, l(3)j1B7, cellular breakdown, HHR6A, Ets, Dhr6, Edg, degradation, protein complex, Zubr1, Affects, Proteins, Rbed1, selective autophagy, function, Client, Endosome, Cell, Contractions, DmelCG2013, Ubiquitin A-52 residue ribosomal protein fusion product 1, MS, native protein, natural protein, Ubiquitin-related 2, MRXS30, Protein, Synthetase, rad6a, ATP-Dependent Proteolysis Factor 1, Receptosomes, pnt-P1, UBC2, pnt-P2, flange, Mass Spectrum Analyses, l(3)s118306, organ process, breakdown of molecule, covalent modifier, Mass Spectrum, biodegradation, ZZ-type zinc finger-containing protein 1, ZUBR1, Protein Gene Products, Mitochondrial Contraction, Gene Proteins, processes, breakdown of substance, Ets58AB, mitochondria, 60S ribosomal protein L40, ligase, cardinality, Ubiquitin-related, ORW1, BcDNA:RE56673, Gm1032, POINT, prevacuolar compartment, CG8705"],"pubmed_title_synonyms":["biochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, cellular breakdown, Lysosome, FGF-induced in gastric cancer, Dhr6, degradation, Zubr1, 6.3.2.-, Kcmf1, CG2013, Rbed1, Gm1666, Synthetases, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, Autolysosome, CEP52, Autolysosomes, cellular catabolism, DEBT91, Human, DmelCG2013, Ubiquitin A-52 residue ribosomal protein fusion product 1, N28143, PSO8, Ubiquitin-related 2, Synthetase, cellular degradation, HMG-20, secretion, ATP-Dependent Proteolysis Factor 1, UBC2, Ubiq, 1700094M07Rik, Ubiquitin, 1810009A16Rik, covalent modifier, Rad6, RAD6, D930005K06Rik, breakdown, High Mobility Protein 20, biodegradation, breakdown of molecule., breakdown of chemical, Debt91, catabolism, RBAF600, Human Ubiquitin, Ubiquitin-related 1, ZZ-type zinc finger-containing protein 1, ZUBR1, Ligase, APF-1, 40S ribosomal protein S27a, breakdown of substance, A930005E13Rik, Pmcf, PCMF, 60S ribosomal protein L40, ligase, ubiquitin, biotransformation, Ubiquitin-related, p600, protein tagging activity, BcDNA:RE56673, Gm1032, mKIAA0462, ZZZ1, Potassium channel modulatory factor, FIGC"],"name_synonyms":["1700094M07Rik, biochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, 1810009A16Rik, cellular breakdown, Rad6, RAD6, D930005K06Rik, Lysosome, breakdown, Dhr6, biodegradation, degradation, breakdown of molecule., breakdown of chemical, Debt91, Zubr1, catabolism, Kcmf1, CG2013, RBAF600, Rbed1, Gm1666, Autolysosome, ZUBR1, Autolysosomes, cellular catabolism, DEBT91, breakdown of substance, DmelCG2013, A930005E13Rik, Pmcf, N28143, PCMF, PSO8, cellular degradation, biotransformation, secretion, p600, BcDNA:RE56673, UBC2, Gm1032, mKIAA0462, ZZZ1, FIGC"],"citation_count":["0"],"additional_accession":["PXD001634"]},"is_claimable":true,"name":"KCMF1 links RAD6 to UBR4 and lysosome-mediated degradation","description":"Raw mass spec. data files, converted peak lists and TPP results files for KCMF1 links RAD6 to UBR4 and lysosome-mediated degradation by Hong et. al, MCP 2014. RAD6 is a ubiquitin E2 protein with roles in a number of different biological processes. Here, using affinity purification coupled with mass spectrometry, we identify a number of new RAD6 binding partners, including the E3 ligase KCMF1 (potassium channel modulatory factor 1). NMR, combined with in vivo and in vitro interaction mapping, demonstrate that the KCMF1 C-terminus binds directly to RAD6, while the N-terminus interacts with vesicle- and mitochondria-associated proteins. KCMF1 and RAD6 co-localize at late endosomes and lysosomes, and cells disrupted for KCMF1 or RAD6 function display defects in vesicle dynamics. Notably, we also find that RAD6A point mutants (R7W and R11Q) found in X-linked intellectual disability (XLID) patients specifically lose the interaction with KCMF1, but not with other previously identified RAD6 interactors. We thus identify a new set of RAD6 interacting partners linked to lysosome-mediated degradation, and highlight specific protein-protein interactions that are lost in some RAD6 XLID mutant proteins.","dates":{"publication":"Thu Jan 01 05:12:00 GMT 2015"},"accession":"MSV000078983","cross_references":{"pubmed":["25582440"]}}