mpidb The Microbial Protein Interaction Database rondelet-2012-1 SurA Is Involved in the Targeting to the Outer Membrane of a Tat Signal Sequence-Anchored Protein. ecolx Escherichia coli far western blotting far western blotting Affinity blotting Affinity blotting western blot western blot Immuno blot Immuno blot Rondelet A., Condemine G. J. Bacteriol. (0021-9193) 2012 Only protein-protein interactions imex curation douet-2009-1 Erwinia chrysanthemi iron metabolism: the unexpected implication of the inner membrane platform within the type II secretion system. dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) anti bait coip anti bait coimmunoprecipitation anti bait coip fingerprinting peptide massfingerprinting fingerprinting Douet V., Expert D., Barras F., Py B. J. Bacteriol. (0021-9193) 2009 Only protein-protein interactions imex curation e0sg38_dicd3 pnlH Dda3937_04108 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MQKNTMPKRTVMPVIDTAFSRRHLLKLAVLLPAFPYARIAQSDSGVTGYAKMKQVSGGGVGGEIVYVNNVKALAFHLGGPAHKNIIITCTLKAPDKYTILLGSNKTLIGQLPGITLYNIYLVSSHNQGNVIIKNMTFLHDKKINGNNDIQLRISSGEGYWLDHCNFMGHEWSVNDGAEDKHIYFGENADFITISNCVFANHRYGCIFGYPVDGNSRFKGKPRITICNNYYHNLYVRAPGLFRYGEFSVFNNVIRGFHLGFTVDGGARVYSSNNHFYSTLKNFSVVDYKQDYLHSQNDSINDQKINKTWGT e0sgc2_dicd3 Chaperone SurA surA Peptidyl-prolyl cis-trans isomerase SurA Rotamase SurA Dda3937_01379 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MKNWRALVLGLALSANMAFAAPQEVNKIAAVVDNSVVLESDINSLLQSVKLNAQEAGQQLPDDATLRHQILERLIMDNIILQMAQKMGVQVTDEQLDRSIANIAAQNRMSVDQLRSRLAAEGVSFDTYRSQIRKDMIIAEVRNSEVRRRVTVLPQEVDSLAQQIASQGASGPEVNLSQILIPLPENPTQDQVDKAESLANRLVKEASQGADFGKLAITYSADPQALKGGQMGWGRPQELPSLFAERLTNPQKGQVIGPIRSGVGFHILRVNDTRGGDQSVSVTEVHARHILLRTSVVMNDAQARARLEDIASQIKSGKLSFTNAAKQLSQDPGTANQGGDLGWSSPDMYDPSFRDALTQLKKGEISAPVHSSFGWHLIQLLDTRQVDKTDAAQKDRAYRMLFNRKFAEEAQTWMQEKRAAAYVKILNGQN e0sg67_dicd3 Protein translocase subunit SecA secA Dda3937_02235 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MLIKLLTKVFGSRNDRALRRMRKIVDVINRLEPDMETLSDDELKAKTQVFRDRIKKGETLESLLPEAFAVVREASKRVFGMRHFDVQLIGGMVLNERCIAEMRTGEGKTLTATLPAYLNALTGRGVHVVTVNDYLAQRDAENNRPLFEFLGLSVGINLPGMPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRELYYALVDEVDSILIDEARTPLIISGPAEDSSELYMRVNKIIPHLIRQEKEDSDTFQGEGHFSVDEKARQVNLTERGLVKIEELLVKGGIMEEGESLYSPANIMLMHHVTAALRAHVLFTRDVDYIVKDDEVIIVDEHTGRTMQGRRWSDGLHQAVEAKENVKINNENQTLASITFQNYFRIYEKLAGMTGTADTEAFEFSSIYKLDTIVVPTNRPMIRKDLPDLVYMTEQEKIGAIIEDIKERTAKGQPVLVGTISIEKSEVVSHALTKAGIKHNVLNAKFHAMEADIVAQAGRSGAVTIATNMAGRGTDIVLGGSWQAEVAQQENPDEAQIAAIKAEWQRRHDDVLAAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDALMRIFASDRVSNMMRKLGMKEGEAIEHPWVTKAIANAQRKVENRNFDIRKQLLEYDDVANDQRRAIYTQRNELLDASDISETINSIREDVFKVTIDAHIPPQSLEEMWDVPGLEQRLKNDFDLELPIAEWLDKEPDLHEETLRERIYAQAVELYGRKEEVVGSDVMRNFEKGVMLQTLDSLWKEHLAAMDYLRQGIHLRGYAQKDPKQEYKRESFAMFAAMLEGLKYEVISTLSKVQVRMPEEVEALEQQRREEAERLARQQQLSHQDEAGSPYADRKIGRNDPCPCGSGKKYKQCHGRLQK e0shd8_dicd3 Periplasmic serine endoprotease DegP-like degQ Dda3937_00697 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MKKTSLLYSALALGIGLSLSSLPPANAALPAVVEGQALPSLAPMLEKVLPAVVSVHVEGTQVQRQRIPEEFKFFFGPNTPSEKQNSRPFEGLGSGVIINAEKGYVLTNNHVVNNADKIQVQLNDGREYDAKLIGRDEQTDIALLQLNDAKNLTEVKMADSDQLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLENFIQTDASINRGNSGGALVNLRGELIGINTAILAPSGGNVGIGFAIPSNMAQNLTQQLVEFGEVKRGLLGIKGSEMTSEIAKAFKVDAQRGAFVSEVIPKSAAAKAGIKAGDVLVSLDGKPISSFAELRAKIGTTAPGKTVRIGLLRDGKQQEVAVVLDNSANVTTNADTLSPALQGATLNNGQLKDGSKGVTIDNVAKDSAAAKVGLQKGDIIVGVNRERVENITQLRKILEAKPSVLALNIVRGDESIYLLLR e0sdc8_dicd3 togA Dda3937_04712 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MAEVIFNKLEKVYSNGFKAVHGIDLTIKDGEFMVIVGPSGCAKSTTLRMLAGLETISGGEVRIGEKIVNNLAPKDRGIAMVFQNYALYPHMTVRENLAFGLKLSKMPKDKIEAQVNEAAKILELEELMDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISDLHKQLKKSGHPATSVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHFPKNMFVAGFIGAPEMNIKPGKLLEENGQITLQVGQYTMSLNQAKQDKVRGYVGKDICFGVRPEYVTVSEAPFDGGHFQGELVRAENMGHEFFMYIKVDGFELTSRMPSDEARVIINNRMNSKVYFKFDMDKCHIFDAKTEQNISL e0sm39_dicd3 General secretion pathway protein F outF Dda3937_02417 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MALFQYQALNAQGKKSQGMQEADSARHARQLLREKGLVPVKIEEQRGEVTTRSGFSLSLRRSHRISASDLALLTRQLATLVAAALPLEEALDAVAKQSEKPKLSALMAAVRAKVVEGHSLAEAMGNFPGSFERLYCAMVAAGEASGHLDAVLNRLADYTEQRQQMRSRIQQAMIYPCVLTLVAISVVSILLSAVVPKVVEQFIHMKQALPLSTRLLMGVSDAVRAYGPWVVLLLVLAVMGFRVLLRQEKHRLVFHRRLLFLPLIGRIARGLNTARYARTLSILNSSAVPLLQAMRISGDVLTNDYARFRLGQATDAVREGVSLHKALEQTSLFPPMMRHMIASGERSGELDGMLTRAADNQDREFSAQMTLALGLFEPLLVVSMAGIVLFIVLAILQPILQLNTLMSM e0sif0_dicd3 acsD Dda3937_02854 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MNNRNHDVLSRMISEKAALHGLLNCLIKEFAIPEGYLRYEWPDEMKGIPPGAYFDGADWKGIPMMIGLPDQLQLFVMVDRRDTFGSQHYLSDVYLRQAQGDWQCPDFEPLVARLLAACEHIAGRKNPELYEQILQSQRLVSAIVSHNGRQRADAPLQHYLQSEQGLWFGHPSHPAPKARLWPAHLGQEQWAPEFQARAALHQFEVPVDGLHIGANGLTPQQVLDGFADQQPASPGHAIICMHPVQAQLFMQDARVQQLLRDNVIRDLGQSGRVASPTASIRTWFIDDHDYFIKGSLNVRITNCVRKNAWYELESTVLIDRLFRQLLDQHADTLGGLVAAAEPGVVSWSPAAAGELDSHWFREQTGGILRENFCRRTGAERSIMAGTLFARGVDLQPMIQTFLRTHYGEALDDNALLYWFDDYQTRLLRPVLSLFFNHGVVMEPHLQNSVLVHQQGRPQQVLLRDFEGVKLTDDLGIRYIDDDIHPRVRQSLLYSREQGWNRIMYCLFINHLSETILALSQGRPQLAPLMWRRVQQQLRAIQGELKQPSPELDALIAGHPVACKTNLKVRLAAEADRQASYVRLPSPWGHAVQHGSEVQHDERRHGDVRHEEARHGEVQHG sura-pnlh 1340318 not-defined-56538530 1340319 unspecified role unspecified role prey prey signal sequence E0SG38-1-41 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminal E0SG38-- gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false not-defined-1192555229 1340320 unspecified role unspecified role bait bait e0sgc2-- E0SGC2-- strep ii tag strep ii tag Strep (II) Strep II Strep (II) Strep II undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Figure 2 outf-acsd-4 1334367 n/a 1334369 unspecified role unspecified role prey prey n/a 1334370 unspecified role unspecified role bait bait n/a 1334371 unspecified role unspecified role prey prey n/a 1334372 unspecified role unspecified role prey prey n/a 1334373 unspecified role unspecified role prey prey association association false false false fig. 1 A tail-specific protease was also identified by name but could not be mapped to a known sequence. DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ gonzalez_gutierrez-2012-1 ecolx Escherichia coli molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Gonzalez-Gutierrez G., Lukk T., Agarwal V., Papke D., Nair SK., Grosman C. DIP original experiment: DIP-251631X Proceedings of the National Academy of Sciences of the United States of America 2012 IMEx Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals. Gonzalez-Gutierrez G., Lukk T., Agarwal V., Papke D., Nair SK., Grosman C. Only protein-protein interactions imex curation gonzalez_gutierrez-2012-2 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Gonzalez-Gutierrez G., Lukk T., Agarwal V., Papke D., Nair SK., Grosman C. DIP original experiment: DIP-251632X Proceedings of the National Academy of Sciences of the United States of America 2012 IMEx Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals. Gonzalez-Gutierrez G., Lukk T., Agarwal V., Papke D., Nair SK., Grosman C. Only protein-protein interactions imex curation bertozzi-2016-1 ecolx Escherichia coli molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Bertozzi C., Zimmermann I., Engeler S., Hilf RJ., Dutzler R. DIP original experiment: DIP-268536X PLoS biology 2016 IMEx Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels. Bertozzi C., Zimmermann I., Engeler S., Hilf RJ., Dutzler R. Only protein-protein interactions imex curation bertozzi-2016-2 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Bertozzi C., Zimmermann I., Engeler S., Hilf RJ., Dutzler R. DIP original experiment: DIP-268537X PLoS biology 2016 IMEx Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels. Bertozzi C., Zimmermann I., Engeler S., Hilf RJ., Dutzler R. Only protein-protein interactions imex curation e0sjq4_dicd3 Dda3937_00520 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MRILWSCCGLVLLLLGLPAWSAPADNAADARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTLMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRCRLAFPLGFLAIGCVLVIRGITL e0sjq4_dicd3-3 3238786 N/A 3238788 unspecified role unspecified role unspecified role unspecified role Mature protein Region 22-343 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false e0sjq4_dicd3-4 3238787 N/A 3238788 unspecified role unspecified role unspecified role unspecified role Mature protein Region 22-343 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false e0sjq4_dicd3-1 3290429 N/A 3238788 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false e0sjq4_dicd3-2 3290430 N/A 3238788 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false UniProt UniProt http://www.uniprot.org loiseau-2003-1 Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Loiseau L., Ollagnier-de-Choudens S., Nachin L., Fontecave M., Barras F. barras@ibsm.cnrs-mrs.fr J. Biol. Chem. 278 (38352-38359) 2003 Only protein-protein interactions imex curation mfontecabve@cea.fr loiseau-2003-3 Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase. in vitro In vitro enzymatic study enzymatic study predetermined predetermined participant predetermined Loiseau L., Ollagnier-de-Choudens S., Nachin L., Fontecave M., Barras F. The activity was assayed from the amount of alanine formed from cysteine or selenocysteine. Selenocysteine solution was obtained after reduction of a 60 mM selenocystine-HCl solution with 10 mM dithiothreitol. barras@ibsm.cnrs-mrs.fr J. Biol. Chem. 278 (38352-38359) 2003 Only protein-protein interactions imex curation mfontecabve@cea.fr loiseau-2003-2 Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase. in vitro In vitro pull down pull down fingerprinting peptide massfingerprinting fingerprinting Loiseau L., Ollagnier-de-Choudens S., Nachin L., Fontecave M., Barras F. barras@ibsm.cnrs-mrs.fr J. Biol. Chem. 278 (38352-38359) 2003 Only protein-protein interactions imex curation mfontecabve@cea.fr sufe_dicd3 Cysteine desulfuration protein SufE Dda3937_03664 sufE protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MAQLPDPQKLLRNFSRCSNWEEKYLYIIELGAGLAPLSDAQRQDGNRVSGCQSQVWIDLASNEQGNVVLHGDSDAAIVKGLIAIVFSLYQGLSVREIVELDVRPFFASLALTQHLTPSRSQGLEAMLRAVRARASALI cysteine small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) sufs_dicd3 Cysteine desulfurase sufS Selenocysteine lyase Selenocysteine reductase Selenocysteine beta-lyase Dda3937_03665 protein protein dicd3 Dickeya dadantii (strain 3937) Erwinia chrysanthemi (strain 3937) MNYPVEHYPIDRVRADFPILQQSVNGQPLAYLDSAASAQKPLAVIDRERDFYLHEYAAVHRGIHTLSARATSAMEEVRAKVATFIHAASAEDIVFVRGTTEAINLVANSYGRTAFQPGDNLVISEMEHHANIVPWQMLAQARGLTLRVLPITDDGELDMAQLPALLDERTRLVAVTQVSNVLGTVNPLAEIIRQAHACGAKVLVDGAQAVMHQAVDVQALDCDFYAFSGHKLYGPSGIGVLYGKSELLQAMPPWEGGGAMIREVSLTQGTTYADPPWRFEAGSPHVAGIIGLGAALDYVSALGVDAIQAHEGLLMRYALASLAEVPTLRLYGPVHRQGVIAFNLGRHHAFDVGSFLDQYGIAIRTGHHCAMPLMSRYGVPSMCRASLALYSCQDEIDRLVAGLHRIHRLLGE sufs-sufe 781456 n/a 781459 unspecified role unspecified role bait bait n/a 781460 unspecified role unspecified role prey prey physical association physical association false false false Fig. 3 sufs-sufe-1 781456 n/a 781460 unspecified role unspecified role bait bait n/a 781459 unspecified role unspecified role prey prey physical association physical association false false false Fig. 3 sufs-sufs 781456 n/a 781460 unspecified role unspecified role prey prey n/a 781460 unspecified role unspecified role bait bait physical association physical association false false false Fig. 3 sufs-cys-sufe 781457 n/a 781460 enzyme enzyme unspecified role unspecified role region 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 false ecoli Escherichia coli (strain K12) n/a 781459 stimulator stimulator unspecified role unspecified role region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region 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 false ecoli Escherichia coli (strain K12) n/a 781461 enzyme target enzyme target substrate substrate unspecified role unspecified role enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction false false false Fig. 5, 6, 7 and Table III. Km and Vmax for cystein are respectively 0.5 mM and 0.9 units/mg. Km and Vmax for selenocystein are respectively 2 mM and 5 units/mg. Temp = 37C sufc-cys-1 781457 n/a 781460 enzyme enzyme unspecified role unspecified role region 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 false ecoli Escherichia coli (strain K12) n/a 781461 enzyme target enzyme target substrate substrate unspecified role unspecified role enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction false false false Fig. 5, 6, 7 and Table III. Km and Vmax for cysteine are respectively 0.5 mM and 0.019 units/mg. Km and Vmax for selenocysteine are respectively 2 mM and 5 units/mg. Temp = 37C sufs-sufe-2 781458 n/a 781459 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region 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 false ecoli Escherichia coli (strain K12) n/a 781460 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 4