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/ Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro protease assay protease assay mudpit multidimensional protein identification technology mudpit Kim S., Grant RA., Sauer RT. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro protease assay protease assay weight by comassie molecular weight estimation by coomasie staining weight by comassie Kim S., Grant RA., Sauer RT. DegP containing the Ser210Ala mutant was denatured in urea, then refolded. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro fps fluorescence polarization spectroscopy Fluorescence anisotropy FPS FPS Fluorescence anisotropy fps tag fluorescence tag visualisation by fluorescence tag fluorescence Kim S., Grant RA., Sauer RT. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti 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 Kim S., Grant RA., Sauer RT. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti 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 Kim S., Grant RA., Sauer RT. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro protease assay protease assay predetermined predetermined participant predetermined Kim S., Grant RA., Sauer RT. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages. Cell (0092-8674) 2011 imex curation Kim S., Grant RA., Sauer RT. bobsauer@mit.edu 26-Sep-2011: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret tag fluorescence tag visualisation by fluorescence tag fluorescence Kim S., Grant RA., Sauer RT. bobsauer@mit.edu Accepted 2011-JUL-06 by JYOTI 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 jyoti Only protein-protein interactions imex curation lysc_chick Lysozyme C LYZ 1,4-beta-N-acetylmuramidase C Allergen Gal d IV protein protein chick Gallus gallus (Chicken) Chicken MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL DIP protein P00698 original sequence version: 158 81E85743FF579468 degp_ecoli Periplasmic serine endoprotease DegP degP htrA ptd b0161 JW0157 Heat shock protein DegP Protease Do protein protein ecoli Escherichia coli (strain K12) MKKTTLALSALALSLGLALSPLSATAAETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQ DIP protein P0C0V0 original sequence version: 94 DIP protein P0C0V0 original sequence version: 75 DIP protein P0C0V0 original sequence version: 62 DIP protein P0C0V0 original sequence version: 84 DIP protein P0C0V0 original sequence version: 67 5482E596F74B6D5F kaspvslgy KASPVSLGY DegP cleavage peptide peptide peptide polypeptide oligopeptide oligopeptide polypeptide chemical synthesis Chemical synthesis (Chemical synthesis) KASPVSLGY degp-kaspvslgy-1 6 10 enzyme target enzyme target substrate substrate neutral component neutral component n-terminal 2-aminobenzoic acid tag tag certain certain sequence position certain certain certain sequence position certain c-terminal nitrated residue nitrated residue Nitro Nitro (NO2) Oxidation to nitro certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 9 enzyme enzyme neutral component neutral component ecoli Escherichia coli (strain K12) 8 stimulator stimulator neutral component neutral component ile-76 required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain P00698:p.[Leu74Tyr;Ile76Val] mutation increasing mutation increasing interaction mutation increasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain L Y certain certain sequence position certain certain certain sequence position certain I V Wed May 02 16:30:50 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'leu74tyr,ile76val' Tue Jun 30 19:44:34 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Leu74Tyr;Ile76Val]' P00698:p.Ala49_Ala50delinsGlyGly mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain AA GG Wed May 02 19:19:49 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ala_ala49-50gly_gly' Tue Jun 30 19:36:25 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ala49_Ala50delinsGlyGly' carboxymethylation modres protein modification ModRes undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain protein cleavage protein cleavage Fig. 1A, Supp. Fig. 1 degp-1 2 9 putative self putative self putative self putative self ecoli Escherichia coli (strain K12) protein cleavage protein cleavage true Fig. 1A degp-lyz-1 2 8 enzyme target enzyme target substrate substrate neutral component neutral component carboxymethylation modres protein modification ModRes undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined P00698:p.Ala49_Ala50delinsGlyGly mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain AA GG Wed May 02 17:30:52 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ala_ala49-50gly_gly' Tue Jun 30 19:45:29 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ala49_Ala50delinsGlyGly' region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ile-76 required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 9 enzyme enzyme neutral component neutral component ecoli Escherichia coli (strain K12) protein cleavage protein cleavage Fig. 1B, Supp. Fig. 3A degp-lyz-2 1 9 enzyme enzyme neutral component neutral component ecoli Escherichia coli (strain K12) 8 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind de novo protein sequence de novo protein sequencing by mass spectrometry de novo protein sequence MS/MS certain certain sequence position certain certain certain sequence position certain carboxymethylation modres protein modification ModRes undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined protein cleavage protein cleavage Fig. 1B degp-lyz-4 5 9 unspecified role unspecified role neutral component neutral component P0C0V0:p.Ser209Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain S A Wed May 02 14:57:35 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser209ala' Tue Jun 30 16:39:37 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ser209Ala' region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) direct interaction direct interaction Table 1 3.76A Rworking = 21.9% Rfree =25% degp-lyz-5 2 9 enzyme enzyme neutral component neutral component denatured denatured P0C0V0:p.Ser209Ala mutation mutation certain certain sequence position certain certain certain sequence position certain S A Wed May 02 15:22:58 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser209ala' Tue Jun 30 17:35:41 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ser209Ala' ecoli Escherichia coli (strain K12) 8 enzyme target enzyme target substrate substrate neutral component neutral component carboxymethylation modres protein modification ModRes undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) protein cleavage protein cleavage Supp. Fig. 2A degp-kaspvslgy-2 6 9 enzyme enzyme neutral component neutral component ecoli Escherichia coli (strain K12) 10 enzyme target enzyme target substrate substrate neutral component neutral component n-terminal 2-aminobenzoic acid tag tag certain certain sequence position certain certain certain sequence position certain c-terminal nitrated residue nitrated residue Nitro Nitro (NO2) Oxidation to nitro certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) protein cleavage protein cleavage Fig. 1A, Supp. Fig. 1 degp-lyz-6 3 9 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0C0V0:p.Ser209Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain S A Wed May 02 16:31:03 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser209ala' Tue Jun 30 16:45:01 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ser209Ala' ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) direct interaction direct interaction Figs. 3C, 3D Binding of DegPS210A to flurescently-labelled 36–76 was initially enhanced and then inhibited by addition of unlabeled 36-76, suggesting that binding is positively cooperative degp-degp 7 9 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept P0C0V0:p.[Cys83Ala;Cys95Ala;Ser236Ala] mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain C A certain certain sequence position certain certain certain sequence position certain S A certain certain sequence position certain certain certain sequence position certain C A Fri Jul 22 11:03:16 BST 2016 This feature has been corrected as a result of our quality control procedures. The original label was 'cys95ala,ser236ala,cys83ala' Wed May 02 14:45:35 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'cys83ala,cys95ala,ser236ala' Tue Jun 30 16:18:54 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Cys83Ala;Cys95Ala;Ser236Ala]' region fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined P0C0V0:p.Tyr470Ala mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain Y A Wed May 02 15:20:39 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'tyr470ala' Tue Jun 30 19:06:36 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Tyr470Ala' ecoli Escherichia coli (strain K12) 8 stimulator stimulator experimental role experimental role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role fluorescence donor fluorescence donor P0C0V0:p.[Cys83Ala;Cys95Ala;Ser236Ala] mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain S A certain certain sequence position certain certain certain sequence position certain C A certain certain sequence position certain certain certain sequence position certain C A Fri Jul 22 10:52:41 BST 2016 This feature has been corrected as a result of our quality control procedures. The original label was 'ser236ala,cys95ala,cys83ala' Wed May 02 18:41:58 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'cys83ala,cys95ala,ser236ala' Tue Jun 30 20:11:53 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Cys83Ala;Cys95Ala;Ser236Ala]' region fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined P0C0V0:p.Tyr470Ala mutation disrupting mutation disrupting interaction mutation disrupting deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Y A Wed May 02 19:10:38 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'tyr470ala' Tue Jun 30 16:18:41 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Tyr470Ala' ecoli Escherichia coli (strain K12) physical association physical association Fig. 4, Supp. FIg. 4B, 4C, 4D, 5A, 5B Active cages assemble rapidly in a reaction that is positively cooperative in substrate concentration, remain stably assembled while uncleaved substrate is present, and dissociate once degradation is complete. degp-degp-1 4 8 stimulator stimulator experimental role experimental role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role fluorescence donor fluorescence donor P0C0V0:p.Ser236Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain S A Wed May 02 18:58:39 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser236ala' Tue Jun 30 19:59:57 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ser236Ala' region fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) physical association physical association Supp. Fig. 4A degp-lyz-7 4 9 unspecified role unspecified role fluorescence donor fluorescence donor P0C0V0:p.Ser236Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain S A Wed May 02 19:05:54 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser236ala' Tue Jun 30 19:06:37 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Ser236Ala' region fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) physical association physical association Supp. Fig. 4A