IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell (0092-8674) 2009 imex curation Simonetta KR., Kazmirski SL., Goedken ER., Cantor AJ., Kelch BA., McNally R., Seyedin SN., Makino DL., O'Donnell M., Kuriyan J. kuriyan@berkeley.edu 01-Sep-2009: Contacted by JYOTI. davet Only protein-protein interactions 2 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Simonetta KR., Kazmirski SL., Goedken ER., Cantor AJ., Kelch BA., McNally R., Seyedin SN., Makino DL., O'Donnell M., Kuriyan J. kuriyan@berkeley.edu Accepted 2009-SEP-18 by DAVET. 01-Sep-2009: Contacted by JYOTI. Cell (0092-8674) 2009 davet Only protein-protein interactions 2 imex curation The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell (0092-8674) 2009 imex curation Simonetta KR., Kazmirski SL., Goedken ER., Cantor AJ., Kelch BA., McNally R., Seyedin SN., Makino DL., O'Donnell M., Kuriyan J. kuriyan@berkeley.edu 01-Sep-2009: Contacted by JYOTI. davet Only protein-protein interactions 2 in vitro In vitro fps fluorescence polarization spectroscopy Fluorescence anisotropy FPS FPS Fluorescence anisotropy fps predetermined predetermined participant predetermined Simonetta KR., Kazmirski SL., Goedken ER., Cantor AJ., Kelch BA., McNally R., Seyedin SN., Makino DL., O'Donnell M., Kuriyan J. kuriyan@berkeley.edu Accepted 2009-SEP-18 by DAVET. 01-Sep-2009: Contacted by JYOTI. Cell (0092-8674) 2009 davet Only protein-protein interactions 2 imex curation The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell (0092-8674) 2009 imex curation Simonetta KR., Kazmirski SL., Goedken ER., Cantor AJ., Kelch BA., McNally R., Seyedin SN., Makino DL., O'Donnell M., Kuriyan J. kuriyan@berkeley.edu 01-Sep-2009: Contacted by JYOTI. davet Only protein-protein interactions 2 in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Simonetta KR., Kazmirski SL., Goedken ER., Cantor AJ., Kelch BA., McNally R., Seyedin SN., Makino DL., O'Donnell M., Kuriyan J. kuriyan@berkeley.edu Accepted 2009-SEP-18 by DAVET. 01-Sep-2009: Contacted by JYOTI. Cell (0092-8674) 2009 davet Only protein-protein interactions 2 imex curation hola_ecoli DNA polymerase III subunit delta b0640 holA JW0635 protein protein ecoli Escherichia coli (strain K12) MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG 87239A678FE16BE2 87239A678FE16BE2 ttttttataggccag TTTTTTATAGGCCAG dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) TTTTTTATAGGCCAG 8C389AFAFC3C39C5 hold_ecoli DNA polymerase III subunit psi holD b4372 JW4334 protein protein ecoli Escherichia coli (strain K12) MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRND DIP protein P28632 original sequence version: 88 DIP protein P28632 original sequence version: null 5B7356201E7E27FE ttgtgggtagataaatacag TTGTGGGTAGATAAATACAGACCTAAGTCCTTGAATGCCGCGTGCGTCCC dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) TTGTGGGTAGATAAATACAGACCTAAGTCCTTGAATGCCGCGTGCGTCCC 865E0C94317E01E1 holb_ecoli DNA polymerase III subunit delta' holB b1099 JW1085 protein protein ecoli Escherichia coli (strain K12) MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL DIP protein P28631 original sequence version: 95 DIP protein P28631 original sequence version: null DC9DAA644AD8A096 adp adenosine 5'-(trihydrogen diphosphate) (ADP) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) gggacgcacgcggcattcaa GGGACGCACGCGGCATTCAAGGACTTAGGTCTGTATT dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) GGGACGCACGCGGCATTCAAGGACTTAGGTCTGTATT B7ABD258A1E51976 trifluoroberyllate(1-) trifluoroberyllate(1−) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) a widely used substitute for the γ-phosphate of ATP a widely used substitute for the γ-phosphate of ATP dpo3x_ecoli DNA polymerase III subunit tau dnaX dnaZ dnaZX b0470 JW0459 DNA polymerase III subunit gamma protein protein ecoli Escherichia coli (strain K12) MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQAPTVPLPETTSQVLAARQQLQRVQGATKAKKSEPAAATRARPVNNAALERLASVTDRVQARPVPSALEKAPAKKEAYRWKATTPVMQQKEVVATPKALKKALEHEKTPELAAKLAAEAIERDPWAAQVSQLSLPKLVEQVALNAWKEESDNAVCLHLRSSQRHLNNRGAQQKLAEALSMLKGSTVELTIVEDDNPAVRTPLEWRQAIYEEKLAQARESIIADNNIQTLRRFFDAELDEESIRPI DIP protein P06710 original sequence version: 106 DIP protein P06710 original sequence version: null D2028BD99E375150 ctggcctata CTGGCCTATA dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) CTGGCCTATA 369722C1AEBEB878 hola-dpo3x-1 1 9 unspecified role unspecified role neutral component neutral component 11 unspecified role unspecified role neutral component neutral component 13 unspecified role unspecified role neutral component neutral component 5 unspecified role unspecified role neutral component neutral component 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association The wild-type E. coli clamp loader complex was crystallized with the ATP analog ADP.BeF3 and primer-template DNA containing a duplex segment of 10 base pairs and a 5 nucleotide 5′ overhang. 3.4A R-factor: 22.34%, Free R-factor: 26.04% Supp. Table 4 hola-dpo3x-2 1 9 unspecified role unspecified role neutral component neutral component 12 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain P06710:p.Thr157Ala mutation mutation certain certain sequence position certain certain certain sequence position certain T A Wed May 02 17:47:04 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'thr157ala' Tue Jun 30 19:26:21 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Thr157Ala' ecoli Escherichia coli (strain K12) 13 unspecified role unspecified role neutral component neutral component 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component 11 unspecified role unspecified role neutral component neutral component physical association physical association The wild-type E. coli clamp loader complex was crystallized with the ATP analog ADP.BeF3 and primer-template DNA containing a duplex segment of 10 base pairs and a 5 nucleotide 5′ overhang. 3.25A R-factor: 22.6%, Free R-factor: 26.3% The Thr157Ala mutation of P06710 prevents ATP hydrolysis. Supp. Table 4 hola-dpo3x-3 1 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association 3.9A R-factor: 35.93%, Free R-factor: 36.14% Supp. Table 6 hola-dpo3x-4 1 11 unspecified role unspecified role neutral component neutral component 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component 13 unspecified role unspecified role neutral component neutral component 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role neutral component neutral component 12 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 6 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association The wild-type E. coli clamp loader complex was crystallized with the ATP analog ADP.BeF3 and primer-template DNA containing a duplex segment of 10 base pairs and a 5 nucleotide 5′ overhang. 3.5A R-factor: 22.34%, Free R-factor: 25.73% Supp. Table 4 dnax-hola-4 2 10 unspecified role unspecified role neutral component neutral component 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component P28630:p.Arg252Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain R A Wed May 02 18:31:25 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg252ala' Tue Jun 30 17:06:34 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg252Ala' P28630:p.Arg248Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain R A Wed May 02 16:35:50 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg248ala' Tue Jun 30 18:22:01 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg248Ala' P28630:p.Lys313Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain K A Wed May 02 16:37:42 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'lys313ala' Tue Jun 30 20:13:24 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Lys313Ala' ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Fluorescence anisotropy data for fluorescently labeled primer-template DNA binding to the wild-type γ complex and five mutants, in the presence of 1 μM β clamp, are shown. Figs. 4B, 6B KD for DNA binding = 1.8E-7M. Mutation of Lys 313 and Arg 248, which interact with the phosphate group of the nucleotide at the -1 position, increases the value of KD to 6.1 E-6M and 1.3 E-6M for the mutants, respectively. Mutation of Arg 252, which interacts with the phosphate group of the nucleotide at the -2 position in the overhang, had a smaller effect (KD = 7.6E-7M). pH=7.5, Temp=25C hola-dpo3x-5 3 12 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 6 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain P28632:p.Trp17Ser mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain W S Wed May 02 16:40:24 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'trp17ser' Tue Jun 30 16:29:33 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Trp17Ser' chemical synthesis Chemical synthesis (Chemical synthesis) 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association Isothermal titration calorimetry data for the binding of the ψ peptide to the clamp loader complex. Fig. 6A Stoichiometry of binding of clamp loader complex to holD peptide is 1:1 Kd=7E-9M (clamp loader binding to holD peptide). pH=7.5, Temp=25C dnax-hola-5 2 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role neutral component neutral component 10 unspecified role unspecified role neutral component neutral component 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 6 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction DNA binding in the presence (blue) and absence (red) of 10 μM ψ peptide is shown. Figs. 6B The values of the KD of DNA binding are 3.8E-7M and 1.8 E-5M in the presence and absence of Psi peptide, respectively. pH=7.5, Temp=25C