MINT MINT, Dpt of Biology, University of Rome Tor Vergata MINT http://mint.bio.uniroma2.it/mint url>http://mint.bio.uniroma2.it/mint/ https://mint.bio.uniroma2.it MINT-[0-9]+ https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac} The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it Structural variability of the ubiquitin specific protease DUSP-UBL double domains. Structural variability of the ubiquitin specific protease DUSP-UBL double domains. FEBS Lett. (0014-5793) 2011 imex curation Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk FEBS Lett. (0014-5793) 2011 Only protein-protein interactions imex curation Structural variability of the ubiquitin specific protease DUSP-UBL double domains. Structural variability of the ubiquitin specific protease DUSP-UBL double domains. FEBS Lett. (0014-5793) 2011 imex curation Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk FEBS Lett. (0014-5793) 2011 Only protein-protein interactions imex curation Structural variability of the ubiquitin specific protease DUSP-UBL double domains. Structural variability of the ubiquitin specific protease DUSP-UBL double domains. FEBS Lett. (0014-5793) 2011 imex curation Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk Only protein-protein interactions in vitro In vitro saxs x ray scattering saxs predetermined predetermined participant predetermined Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk FEBS Lett. (0014-5793) 2011 Only protein-protein interactions imex curation Structural variability of the ubiquitin specific protease DUSP-UBL double domains. Structural variability of the ubiquitin specific protease DUSP-UBL double domains. FEBS Lett. (0014-5793) 2011 imex curation Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk Only protein-protein interactions in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Elliott PR., Liu H., Pastok MW., Grossmann GJ., Rigden DJ., Clague MJ., Urbé S., Barsukov IL. suggested by lperfetto P.R.Elliott@liv.ac.uk FEBS Lett. (0014-5793) 2011 Only protein-protein interactions imex curation ubp4_human Ubiquitin carboxyl-terminal hydrolase 4 Ubiquitin-specific-processing protease 4 Deubiquitinating enzyme 4 Ubiquitous nuclear protein homolog USP4 UNP UNPH Ubiquitin thioesterase 4 protein protein human Homo sapiens Human MAEGGGCRERPDAETQKSELGPLMRTTLQRGAQWYLIDSRWFKQWKKYVGFDSWDMYNVGEHNLFPGPIDNSGLFSDPESQTLKEHLIDELDYVLVPTEAWNKLLNWYGCVEGQQPIVRKVVEHGLFVKHCKVEVYLLELKLCENSDPTNVLSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTVQDAGLYQGQVLVIEPQNEDGTWPRQTLQSKSSTAPSRNFTTSPKSSASPYSSVSASLIANGDSTSTCGMHSSGVSRGGSGFSASYNCQEPPSSHIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEFYKTPSLSSSGSSDGGTRPSSSQQGFGDDEACSMDTN 63055C9ADFE36713 ubp11_human Ubiquitin carboxyl-terminal hydrolase 11 USP11 UHX1 Ubiquitin-specific-processing protease 11 Deubiquitinating enzyme 11 Ubiquitin thioesterase 11 protein protein human Homo sapiens Human MAVAPRLFGGLCFRFRDQNPEVAVEGRLPISHSCVGCRRERTAMATVAANPAAAAAAVAAAAAVTEDREPQHEELPGLDSQWRQIENGESGRERPLRAGESWFLVEKHWYKQWEAYVQGGDQDSSTFPGCINNATLFQDEINWRLKEGLVEGEDYVLLPAAAWHYLVSWYGLEHGQPPIERKVIELPNIQKVEVYPVELLLVRHNDLGKSHTVQFSHTDSIGLVLRTARERFLVEPQEDTRLWAKNSEGSLDRLYDTHITVLDAALETGQLIIMETRKKDGTWPSAQLHVMNNNMSEEDEDFKGQPGICGLTNLGNTCFMNSALQCLSNVPQLTEYFLNNCYLEELNFRNPLGMKGEIAEAYADLVKQAWSGHHRSIVPHVFKNKVGHFASQFLGYQQHDSQELLSFLLDGLHEDLNRVKKKEYVELCDAAGRPDQEVAQEAWQNHKRRNDSVIVDTFHGLFKSTLVCPDCGNVSVTFDPFCYLSVPLPISHKRVLEVFFIPMDPRRKPEQHRLVVPKKGKISDLCVALSKHTGISPERMMVADVFSHRFYKLYQLEEPLSSILDRDDIFVYEVSGRIEAIEGSREDIVVPVYLRERTPARDYNNSYYGLMLFGHPLLVSVPRDRFTWEGLYNVLMYRLSRYVTKPNSDDEDDGDEKEDDEEDKDDVPGPSTGGSLRDPEPEQAGPSSGVTNRCPFLLDNCLGTSQWPPRRRRKQLFTLQTVNSNGTSDRTTSPEEVHAQPYIAIDWEPEMKKRYYDEVEAEGYVKHDCVGYVMKKAPVRLQECIELFTTVETLEKENPWYCPSCKQHQLATKKLDLWMLPEILIIHLKRFSYTKFSREKLDTLVEFPIRDLDFSEFVIQPQNESNPELYKYDLIAVSNHYGGMRDGHYTTFACNKDSGQWHYFDDNSVSPVNENQIESKAAYVLFYQRQDVARRLLSPAGSSGAPASPACSSPPSSEFMDVN DIP protein P51784 original sequence version: 155 876FDC41945AFD9B ubp15_human Ubiquitin carboxyl-terminal hydrolase 15 Unph4 USP15 KIAA0529 Ubiquitin-specific-processing protease 15 Deubiquitinating enzyme 15 Unph-2 Ubiquitin thioesterase 15 protein protein human Homo sapiens Human MAEGGAADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPRGPSTPKSPGASNFSTLPKISPSSLSNNYNNMNNRNVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNILDLCTALSALSGIPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLMAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEDTCKGQLTGHKKRLFTFQFNNLGNTDINYIKDDTRHIRFDDRQLRLDERSFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPINDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGFFPLDRETKGASAATGIPLESDEDSNDNDNDIENENCMHTN DIP protein Q9Y4E8 original sequence version: 128 E81FEB9DE57F7089 usp15-1 1 USP15 7 western blot western blot Immuno blot Immuno blot predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 2.0 direct interaction direct interaction mint f1b sf1 Superpositions of the SEC-MALLS elution profiles for USP4, 11 and 15 DUSP-UBL double domains generated in a series of dilutions. For all proteins, apart from USP4, elution profiles and molecular weights do not change with concentrations and the measured molecular weights show that USP11 is a monomer and USP15 can form stable monomer and dimer. For USP4 the measured molecular weight is intermediate between that of the monomer and dimer. The effective molecular weight decreases with concentration and across the peak, demonstrating a dynamic equilibrium. Additionally, the maximum of the peak shifts to the higher volume with the decrease of the concentration and the peak shapes at high concentrations are non-symmetrical, with tailing at high volumes. These concentration changes and the molecular weight values demonstrate a dynamic exchange between monomer and dimer for USP4. In the first run at the highest concentration we detected minor, high molecular weight species for USP4 and USP11 (~9.5 ml elution volume) that have molecular masses of ~90 kDa and ~50 kDa (USPs 4 and 11 respectively). This is consistent with a tetrameric form for USP4 and dimeric form for USP11. In addition, the USP15 dimer contained a shoulder that was consistent with a tetrameric form with an experimental molecular mass of ~100 kDa. SDS-PAGE (shown) confirms that the minor forms are oligomeric forms of the corresponding proteins. In subsequent runs the minor forms were absent, showing a lack of exchange between the major and minor forms. These minor forms are likely representing a small amount (~5%) of aggregated protein. usp15-1 1 USP15 7 western blot western blot Immuno blot Immuno blot predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 4.0 direct interaction direct interaction sf1 mint Superpositions of the SEC-MALLS elution profiles for USP4, 11 and 15 DUSP-UBL double domains generated in a series of dilutions. For all proteins, apart from USP4, elution profiles and molecular weights do not change with concentrations and the measured molecular weights show that USP11 is a monomer and USP15 can form stable monomer and dimer. For USP4 the measured molecular weight is intermediate between that of the monomer and dimer. The effective molecular weight decreases with concentration and across the peak, demonstrating a dynamic equilibrium. Additionally, the maximum of the peak shifts to the higher volume with the decrease of the concentration and the peak shapes at high concentrations are non-symmetrical, with tailing at high volumes. These concentration changes and the molecular weight values demonstrate a dynamic exchange between monomer and dimer for USP4. In the first run at the highest concentration we detected minor, high molecular weight species for USP4 and USP11 (~9.5 ml elution volume) that have molecular masses of ~90 kDa and ~50 kDa (USPs 4 and 11 respectively). This is consistent with a tetrameric form for USP4 and dimeric form for USP11. In addition, the USP15 dimer contained a shoulder that was consistent with a tetrameric form with an experimental molecular mass of ~100 kDa. SDS-PAGE (shown) confirms that the minor forms are oligomeric forms of the corresponding proteins. In subsequent runs the minor forms were absent, showing a lack of exchange between the major and minor forms. These minor forms are likely representing a small amount (~5%) of aggregated protein. usp4-3 1 USP4 5 western blot western blot Immuno blot Immuno blot predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 2.0 direct interaction direct interaction mint sf1 f1b Superpositions of the SEC-MALLS elution profiles for USP4, 11 and 15 DUSP-UBL double domains generated in a series of dilutions. For all proteins, apart from USP4, elution profiles and molecular weights do not change with concentrations and the measured molecular weights show that USP11 is a monomer and USP15 can form stable monomer and dimer. For USP4 the measured molecular weight is intermediate between that of the monomer and dimer. The effective molecular weight decreases with concentration and across the peak, demonstrating a dynamic equilibrium. Additionally, the maximum of the peak shifts to the higher volume with the decrease of the concentration and the peak shapes at high concentrations are non-symmetrical, with tailing at high volumes. These concentration changes and the molecular weight values demonstrate a dynamic exchange between monomer and dimer for USP4. In the first run at the highest concentration we detected minor, high molecular weight species for USP4 and USP11 (~9.5 ml elution volume) that have molecular masses of ~90 kDa and ~50 kDa (USPs 4 and 11 respectively). This is consistent with a tetrameric form for USP4 and dimeric form for USP11. In addition, the USP15 dimer contained a shoulder that was consistent with a tetrameric form with an experimental molecular mass of ~100 kDa. SDS-PAGE (shown) confirms that the minor forms are oligomeric forms of the corresponding proteins. In subsequent runs the minor forms were absent, showing a lack of exchange between the major and minor forms. These minor forms are likely representing a small amount (~5%) of aggregated protein. usp4-3 1 USP4 5 western blot western blot Immuno blot Immuno blot predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 4.0 direct interaction direct interaction sf1 mint Superpositions of the SEC-MALLS elution profiles for USP4, 11 and 15 DUSP-UBL double domains generated in a series of dilutions. For all proteins, apart from USP4, elution profiles and molecular weights do not change with concentrations and the measured molecular weights show that USP11 is a monomer and USP15 can form stable monomer and dimer. For USP4 the measured molecular weight is intermediate between that of the monomer and dimer. The effective molecular weight decreases with concentration and across the peak, demonstrating a dynamic equilibrium. Additionally, the maximum of the peak shifts to the higher volume with the decrease of the concentration and the peak shapes at high concentrations are non-symmetrical, with tailing at high volumes. These concentration changes and the molecular weight values demonstrate a dynamic exchange between monomer and dimer for USP4. In the first run at the highest concentration we detected minor, high molecular weight species for USP4 and USP11 (~9.5 ml elution volume) that have molecular masses of ~90 kDa and ~50 kDa (USPs 4 and 11 respectively). This is consistent with a tetrameric form for USP4 and dimeric form for USP11. In addition, the USP15 dimer contained a shoulder that was consistent with a tetrameric form with an experimental molecular mass of ~100 kDa. SDS-PAGE (shown) confirms that the minor forms are oligomeric forms of the corresponding proteins. In subsequent runs the minor forms were absent, showing a lack of exchange between the major and minor forms. These minor forms are likely representing a small amount (~5%) of aggregated protein. usp15-1 1 USP15 7 western blot western blot Immuno blot Immuno blot predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component partially purified partially purified Stoichiometry: 2.0 physical association physical association f3b mint usp11-1 1 USP11 6 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 2.0 direct interaction direct interaction sf1 mint Superpositions of the SEC-MALLS elution profiles for USP4, 11 and 15 DUSP-UBL double domains generated in a series of dilutions. For all proteins, apart from USP4, elution profiles and molecular weights do not change with concentrations and the measured molecular weights show that USP11 is a monomer and USP15 can form stable monomer and dimer. For USP4 the measured molecular weight is intermediate between that of the monomer and dimer. The effective molecular weight decreases with concentration and across the peak, demonstrating a dynamic equilibrium. Additionally, the maximum of the peak shifts to the higher volume with the decrease of the concentration and the peak shapes at high concentrations are non-symmetrical, with tailing at high volumes. These concentration changes and the molecular weight values demonstrate a dynamic exchange between monomer and dimer for USP4. In the first run at the highest concentration we detected minor, high molecular weight species for USP4 and USP11 (~9.5 ml elution volume) that have molecular masses of ~90 kDa and ~50 kDa (USPs 4 and 11 respectively). This is consistent with a tetrameric form for USP4 and dimeric form for USP11. In addition, the USP15 dimer contained a shoulder that was consistent with a tetrameric form with an experimental molecular mass of ~100 kDa. SDS-PAGE (shown) confirms that the minor forms are oligomeric forms of the corresponding proteins. In subsequent runs the minor forms were absent, showing a lack of exchange between the major and minor forms. These minor forms are likely representing a small amount (~5%) of aggregated protein. usp15-1 2 USP15 7 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 2.0 direct interaction direct interaction mint t1 f1d sf2 PDB code:3PV1 usp15-1 3 USP15 7 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP Stoichiometry: 2.0 direct interaction direct interaction sf3b mint usp4-usp4 4 USP4 5 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP USP4 5 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified binding site binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain DUSP direct interaction direct interaction homomint mint sf4b [1H, 15N] HSQC spectra of the DUSP-UBL domains shows uniform, well dispersed cross-peaks for monomeric USP15 DUSP-UBL and also USP11. Although we were unable to obtain a structure of the USP11 DUSP-UBL double domain, the spectra are in agreement with a well folded protein for USP11. The USP4 cross-peaks on the other hand are dispersed but suffer from extensive line broadening, consistent with a higher oligomeric state in solution.