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/ keyamura-2011-1 DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA. in vitro In vitro filter binding filter binding Filter overlay assay Filter overlay assay autoradiography autoradiography Keyamura K., Katayama T. katayama@phar.kyushu-u.ac.jp J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation keyamura-2011-2 DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA. in vitro In vitro atpase assay atpase assay predetermined predetermined participant predetermined Keyamura K., Katayama T. "Nucleotides bound to DnaA were recovered on a nitrocellulose filter, separated by thin-layer chromatography, and quantified by a BAS2500 imaging analyzer (Fujifilm)." katayama@phar.kyushu-u.ac.jp J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation keyamura-2011-3 DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA. in vitro In vitro anti tag coip anti tag coimmunoprecipitation anti tag coip weight silver stain molecular weight estimation by silver staining weight silver stain Keyamura K., Katayama T. katayama@phar.kyushu-u.ac.jp J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation keyamura-2011-4 DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Keyamura K., Katayama T. katayama@phar.kyushu-u.ac.jp J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation keyamura-2011-5 DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA. ecoli Escherichia coli (strain K12) anti tag coip anti tag coimmunoprecipitation anti tag coip weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Keyamura K., Katayama T. katayama@phar.kyushu-u.ac.jp J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation atp ATP Adenosine 5'-triphosphate Adenosine triphosphate ADENOSINE-5'-TRIPHOSPHATE Adephos Adetol Adynol Atipi ATP Atriphos Cardenosine Fosfobion Glucobasin H4atp Myotriphos Triadenyl Triphosphaden adenosine 5'-(tetrahydrogen triphosphate) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) dnaa_ecoli Chromosomal replication initiator protein DnaA dnaA b3702 JW3679 protein protein ecoli Escherichia coli (strain K12) MSLSLWQQCLARLQDELPATEFSMWIRPLQAELSDNTLALYAPNRFVLDWVRDKYLNNINGLLTSFCGADAPQLRFEVGTKPVTQTPQAAVTSNVAAPAQVAQTQPQRAAPSTRSGWDNVPAPAEPTYRSNVNVKHTFDNFVEGKSNQLARAAARQVADNPGGAYNPLFLYGGTGLGKTHLLHAVGNGIMARKPNAKVVYMHSERFVQDMVKALQNNAIEEFKRYYRSVDALLIDDIQFFANKERSQEEFFHTFNALLEGNQQIILTSDRYPKEINGVEDRLKSRFGWGLTVAIEPPELETRVAILMKKADENDIRLPGEVAFFIAKRLRSNVRELEGALNRVIANANFTGRAITIDFVREALRDLLALQEKLVTIDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS adp adenosine 5'-(trihydrogen diphosphate) (ADP) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) hda_ecoli DnaA regulatory inactivator Hda hda yfgE DnaA paralog idaB f248c JW5397 b2496 protein protein ecoli Escherichia coli (strain K12) MNTPAQLSLPLYLPDDETFASFWPGDNSSLLAALQNVLRQEHSGYIYLWAREGAGRSHLLHAACAELSQRGDAVGYVPLDKRTWFVPEVLDGMEHLSLVCIDNIECIAGDELWEMAIFDLYNRILESGKTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEDKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRKLTIPFVKEILKL 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 This sequence has been withdrawn from Uniprot. dnaa-atp 1372162 n/a 1372167 unspecified role unspecified role prey prey region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1372168 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false 1372162 Fig. 2 dnaa-adp 1372162 n/a 1372169 unspecified role unspecified role prey prey region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 n/a 1372168 unspecified role unspecified role bait bait P03004:p.Leu422Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Pro423Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Fig. 2b dnaa-atp 1372163 n/a 1372167 cofactor cofactor coenzyme unspecified role unspecified role region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1372168 enzyme enzyme unspecified role unspecified role ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 2d dnaa-hda-atp 1372163 n/a 1372170 unspecified role unspecified role unspecified role unspecified role c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecoli Escherichia coli (strain K12) n/a 1372168 enzyme enzyme unspecified role unspecified role P03004:p.Pro423Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Leu422Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false P03004:p.Leu422Gly mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1372167 cofactor cofactor coenzyme unspecified role unspecified role region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) atpase reaction atpase reaction false false false Fig. 2c, e dnaa-hda-beta_clamp 1372164 n/a 1372168 enzyme enzyme prey prey P03004:p.Leu422Gly mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Leu422Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Pro423Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1372171 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1372170 enzyme enzyme bait bait c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P69931:p.Gln6Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 4a hda-beta 1372164 n/a 1372171 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1372170 enzyme enzyme bait bait c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 4a hda-dnaa 1372165 n/a 1372170 enzyme enzyme bait bait c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecoli Escherichia coli (strain K12) n/a 1372168 enzyme enzyme prey prey P03004:p.Leu422Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Leu422Gly mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Pro423Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 4b, c dnaa-atp-adp 1372166 n/a 1372169 unspecified role unspecified role prey prey region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1372167 unspecified role unspecified role prey prey region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1372168 enzyme enzyme prey prey P03004:p.Pro423Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Leu422Gly mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P03004:p.Leu422Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 6