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/ http://www.ebi.ac.uk/ kozlov-2010-1 Binding specificity of Escherichia coli single-stranded DNA binding protein for the chi subunit of DNA pol III holoenzyme and PriA helicase. in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Kozlov A.G., Jezewska M.J., Bujalowski W., Lohman T.M. The ssDNA consisted of several (dT) constructs, either 20, 35 or 75 base pairs long. As the two proteins under investigations were either binding or not binding in an assay, the constructs were combined into one interaction per interactor combination. lohman@ biochem.wustl.edu lohman@biochem.wustl.edu [NaCl] length of (dT) Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation holc_ecoli DNA polymerase III subunit chi holC b4259 JW4216 protein protein ecoli Escherichia coli (strain K12) MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK 7FEFFC359B28AA88 ssb_ecoli Single-stranded DNA-binding protein Helix-destabilizing protein ssb exrB lexC b4059 JW4020 protein protein ecoli Escherichia coli (strain K12) MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF dt-dna oligo(dT) dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) pria_ecoli Primosomal protein N' priA b3935 Replication factor Y JW3906 ATP-dependent helicase PriA protein protein ecoli Escherichia coli (strain K12) MPVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQERIGIVVSVSDASELPLNELKAVVEVLDSEPVFTHSVWRLLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRDQVATLEFNDAALQALRKKGLCDLASETPEFSDWRTNYAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHHLRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPGVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLILSSPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIINGTLALINTIPDSRKVKWVLDVDPIEG ssb-holc-2 1420929 n/a 1420930 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 1420931 unspecified role unspecified role neutral component neutral component 170-178 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P0AGE0:p.Pro177Ser mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false P0AGE0:p.Pro169Trp mutation mutation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 direct interaction direct interaction false false false pH 7.5, 10% glycerol, 25C, or pH 7.0, 25% glycerol, 25C Fig.s 2, 3, 4, Tables 1, 2 0.02 or 0.2 M (no change in interaction) dt_dna-pria 1420929 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1420933 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 3.0 direct interaction direct interaction false false false pH 7.0, 25% glycerol, 25C Table 2 70 nt 0.2 M dt_dna-pria-1 1420929 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1420933 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 1420931 unspecified role unspecified role neutral component neutral component 170-178 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P0AGE0:p.Pro169Trp mutation mutation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false pH 7.0, 25% glycerol, 25C Fig. 5b 0.2 M 20 nt ssb-pria 1420929 n/a 1420931 unspecified role unspecified role neutral component neutral component P0AGE0:p.Pro177Ser mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false P0AGE0:p.Pro169Trp mutation mutation certain certain sequence position certain certain certain sequence position certain false 170-178 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1420933 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false pH 7.5, 10% glycerol, 25C, or pH 7.0, 25% glycerol, 25C Fig.s 3, 4, Table 1, 2 0.02 or 0.2 M (interaction doesn't change) dt_dna-ssb 1420929 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1420931 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 direct interaction direct interaction false false false pH 7.0, 25% glycerol, 25C Fig. 6a 0.2 NaCl 70 nt ssb-holc-1 1420929 n/a 1420931 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1420930 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 direct interaction direct interaction false false false pH 7.0, 25% glycerol, 25C Fig. 6b, Table 2 0.2 M dt_dna-pria-2 1420929 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1420933 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false pH 7.0, 25% glycerol, 25C Fig. 5a, Table 2 20 nt 0.2 M dt_dna-ssb-1 1420929 n/a 1420931 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 8.0 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 direct interaction direct interaction false false false pH 7.0, 25% glycerol, 25C Fig. 6a 0.02 NaCl 70 nt dt_dna-ssb-2 1420929 n/a 1420931 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 direct interaction direct interaction false false false pH 7.0, 25% glycerol, 25C Fig. 6a 0.02 NaCl 70 nt dt_dna-ssb-3 1420929 n/a 1420930 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 n/a 1420931 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 physical association physical association false false false pH 7.0, 25% glycerol, 25C, or pH 8.1, 25C Fig. 6b, 6c, Table 2 0.02 M 70 nt holc-dt_dna-1 1420929 n/a 1420931 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 4.0 n/a 1420930 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 physical association physical association false false false pH 7.0, 25% glycerol, 25C Fig. 6d, Table 2 0.2 M 70 nt dt_dna-pria-3 1420929 n/a 1420931 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 n/a 1420933 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 n/a 1420932 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 physical association physical association false false false pH 7.0, 25% glycerol, 25C Fig. 7, Table 2 0.2 M 70 nt Stoichiometry for PriA =4 in text but =3 in Table 2! The modelled stoichiometry in Fig. 8 suggests that it most likely =4. Stoichiometry for PriA with SSB-(dT)35 was difficult to calculate but a model suggests that it is most likely =2 (see Fig.8). pria-ssb 1420929 n/a 1420933 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 1420931 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association false false false pH 7.0, 25% glycerol, 25C Fig. 7, Table 2 0.2 M