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 Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J. (0261-4189) 2013 imex curation Toste Rêgo A., Holding AN., Kent H., Lamers MH. suggested by lperfetto Only protein-protein interactions in vitro In vitro crosslink cross-linking study crosslink ms participant Identification by mass spectrometry ms participant Toste Rêgo A., Holding AN., Kent H., Lamers MH. suggested by lperfetto EMBO J. (0261-4189) 2013 Only protein-protein interactions imex curation Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J. (0261-4189) 2013 imex curation Toste Rêgo A., Holding AN., Kent H., Lamers MH. suggested by lperfetto Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Toste Rêgo A., Holding AN., Kent H., Lamers MH. suggested by lperfetto EMBO J. (0261-4189) 2013 Only protein-protein interactions imex curation dpo3a_ecoli DNA polymerase III subunit alpha dnaE polC b0184 JW0179 protein protein ecoli Escherichia coli (strain K12) MSEPRFVHLRVHSDYSMIDGLAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPTGDMSTEDYLVKRAKEGLEERLAFLFPDEEERLKRRPEYDERLETELQVINQMGFPGYFLIVMEFIQWSKDNGVPVGPGRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSMPDFDVDFCMEKRDQVIEHVADMYGRDAVSQIITFGTMAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPGMTLAKAFEAEPQLPEIYEADEEVKALIDMARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPVTQFDKSDVEYAGLVKFDFLGLRTLTIINWALEMINKRRAKNGEPPLDIAAIPLDDKKSFDMLQRSETTAVFQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVDNFIDRKHGREEISYPDVQWQHESLKPVLEPTYGIILYQEQVMQIAQVLSGYTLGGADMLRRAMGKKKPEEMAKQRSVFAEGAEKNGINAELAMKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHYPAEFMAAVMTADMDNTEKVVGLVDECWRMGLKILPPDINSGLYHFHVNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIMSGAFDRLGPHRAALMNSLGDALKAADQHAKAEAIGQADMFGVLAEEPEQIEQSYASCQPWPEQVVLDGERETLGLYLTGHPINQYLKEIERYVGGVRLKDMHPTERGKVITAAGLVVAARVMVTKRGNRIGICTLDDRSGRLEVMLFTDALDKYQQLLEKDRILIVSGQVSFDDFSGGLKMTAREVMDIDEAREKYARGLAISLTDRQIDDQLLNRLRQSLEPHRSGTIPVHLYYQRADARARLRFGATWRVSPSDRLLNDLRGLIGSEQVELEFD DIP protein P10443 original sequence version: 103 DIP protein P10443 original sequence version: null 1A4F75F373841716 dpo4_ecoli DNA polymerase IV Translesion synthesis polymerase IV dinB dinP b0231 JW0221 protein protein ecoli Escherichia coli (strain K12) MRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDPQMERQLVLGL 74DF44DCA18D405F dpo3b_ecoli Beta sliding clamp dnaN Beta-clamp processivity factor DNA polymerase III beta sliding clamp subunit JW3678 b3701 protein protein ecoli Escherichia coli (strain K12) MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL DIP protein P0A988 original sequence version: 48 This sequence has been withdrawn from Uniprot. 7A45646F61255B5A dpo3e_ecoli DNA polymerase III subunit epsilon dnaQ mutD b0215 JW0205 protein protein ecoli Escherichia coli (strain K12) MSTAITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSMAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQKKGGSCLWRA DIP protein P03007 original sequence version: 106 DIP protein P03007 original sequence version: null 4211C9A00744964F dnae-dnan-1 2 DNA Pol III 3 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined undefined mutation mutation disrupting interaction mutation disrupting mutation disrupting interaction mutation disrupting deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Wed Jul 06 17:43:16 BST 2016 Sequence change details about this feature cannot be ascertained or do not fit with the current version of the referenced protein, so they have been deleted as a result of our quality control procedures. The original label was 'mutation disrupting' 917 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Exonuclease 6 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association mint f1 f6 At higher concentrations (5 mM), almost half of the clamp comigrates with the Pol III, while at 10 mM the two proteins form an almost single complex. Strikingly, in the presence of the exonuclease (Figure 1, bottom row) the interaction between Pol III and clamp is enhanced, as shown by the co-migration of the clamp in the Pol III exonuclease complex even at the lowest concentration (1.5 mM). At higher concentrations (5 10 mM), the complex is further enhanced, ultimately creating a robust complex. We also tested the effect of y, a small non-essential protein that binds to the exonuclease. We find that the addition of y has no effect on the migration pattern of the Pol III clamp exonuclease complex even though it co-migrates with the complex (Supplementary Figure S1B). dnae-dnan-1 2 DNA Pol III 3 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined undefined mutation mutation decreasing interaction mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Wed Jul 06 17:43:24 BST 2016 Sequence change details about this feature cannot be ascertained or do not fit with the current version of the referenced protein, so they have been deleted as a result of our quality control procedures. The original label was 'mutation decreasing' 923-924 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction mint f1 f6 Interestingly, mutation of the internal clamp binding motif of Pol III decreased binding (Figure 6B), but does not abolish it, suggesting that the tail of Pol III may have more than one site of interaction with the clamp dnae-dnan-1 2 DNA Pol III 3 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified undefined mutation mutation disrupting interaction mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Wed Jul 06 17:12:24 BST 2016 Sequence change details about this feature cannot be ascertained or do not fit with the current version of the referenced protein, so they have been deleted as a result of our quality control procedures. The original label was 'mutation disrupting' 956 his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Exonuclease 6 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association mint f1 f6 At higher concentrations (5 mM), almost half of the clamp comigrates with the Pol III, while at 10 mM the two proteins form an almost single complex. Strikingly, in the presence of the exonuclease (Figure 1, bottom row) the interaction between Pol III and clamp is enhanced, as shown by the co-migration of the clamp in the Pol III exonuclease complex even at the lowest concentration (1.5 mM). At higher concentrations (5 10 mM), the complex is further enhanced, ultimately creating a robust complex. We also tested the effect of y, a small non-essential protein that binds to the exonuclease. We find that the addition of y has no effect on the migration pattern of the Pol III clamp exonuclease complex even though it co-migrates with the complex (Supplementary Figure S1B). dnae-dnan-1 2 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined DNA Pol III 3 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified undefined mutation mutation decreasing interaction mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Wed Jul 06 17:12:39 BST 2016 Sequence change details about this feature cannot be ascertained or do not fit with the current version of the referenced protein, so they have been deleted as a result of our quality control procedures. The original label was 'mutation decreasing' 917 his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction mint f1 f6 Interestingly, mutation of the internal clamp binding motif of Pol III decreased binding (Figure 6B), but does not abolish it, suggesting that the tail of Pol III may have more than one site of interaction with the clamp dnae-dnan-1 2 DNA Pol III 3 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined undefined mutation mutation decreasing interaction mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Wed Jul 06 17:43:04 BST 2016 Sequence change details about this feature cannot be ascertained or do not fit with the current version of the referenced protein, so they have been deleted as a result of our quality control procedures. The original label was 'mutation decreasing' 956 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction mint f1 f6 Interestingly, mutation of the internal clamp binding motif of Pol III decreased binding (Figure 6B), but does not abolish it, suggesting that the tail of Pol III may have more than one site of interaction with the clamp dnae-dnan-1 2 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined DNA Pol III 3 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined undefined mutation mutation decreasing interaction mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Wed Jul 06 17:10:53 BST 2016 Sequence change details about this feature cannot be ascertained or do not fit with the current version of the referenced protein, so they have been deleted as a result of our quality control procedures. The original label was 'mutation decreasing' 975 direct interaction direct interaction mint f1 f6 Interestingly, mutation of the internal clamp binding motif of Pol III decreased binding (Figure 6B), but does not abolish it, suggesting that the tail of Pol III may have more than one site of interaction with the clamp dinb-dnan-2 2 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined DNA Pol IV 4 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association f7 mint we analysed the interactions of the clamp, Pol III, and Pol IV, in absence and presence of the exonuclease (Figure 7). Alone, Pol IV readily forms a complex with the clamp, which is not disrupted by addition of the exonuclease (Figure 7A, bottom panel). dnan-dnaq-7 2 Clamp 5 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Exonuclease 6 weight by comassie molecular weight estimation by coomasie staining weight by comassie experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined P03007:p.Phe187Ala mutation disrupting interaction mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain F A Tue Jul 12 10:54:23 BST 2016 This feature has been corrected as a result of our quality control procedures. The original label was 'mutation disrupting' Wed May 02 15:35:14 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'phe187ala' Tue Jun 30 18:32:57 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Phe187Ala' P03007:p.Met185Ala mutation disrupting interaction mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain M A Tue Jul 12 10:15:54 BST 2016 This feature has been corrected as a result of our quality control procedures. The original label was 'mutation disrupting' Wed May 02 16:19:35 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'met185ala' Tue Jun 30 16:56:35 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Met185Ala' direct interaction direct interaction f3 mint We already showed that the mutation of the clamp binding motif in the exonuclease results in a loss of clamp binding (Figure 3) dnae-dnan-1 1 DNA Pol III 3 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Clamp 5 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Exonuclease 6 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association mint t1 sf2 dnae-dnan-1 1 DNA Pol III 3 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined Clamp 5 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction mint t1 sf2 dnae-dnaq-1 1 Exonuclease 6 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined DNA Pol III 3 ms participant Identification by mass spectrometry ms participant experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction mint t1 sf2