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/ zhang-2012b-3 MutL associates with Escherichia coli RecA and inhibits its ATPase activity. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Zhang M., Zhou Y., Li T., Wang H., Cheng F., Zhou Y., Bi L., Zhang X.E. blj@sun5.ibp.ac.cn, x.zhang@wh.iov.cn Arch. Biochem. Biophys. (0003-9861) 2012 Only protein-protein interactions imex curation zhang-2012b-5 MutL associates with Escherichia coli RecA and inhibits its ATPase activity. in vitro In vitro atpase assay atpase assay predetermined predetermined participant predetermined Zhang M., Zhou Y., Li T., Wang H., Cheng F., Zhou Y., Bi L., Zhang X.E. blj@sun5.ibp.ac.cn, x.zhang@wh.iov.cn Arch. Biochem. Biophys. (0003-9861) 2012 Only protein-protein interactions imex curation zhang-2012b-1 MutL associates with Escherichia coli RecA and inhibits its ATPase activity. in vitro In vitro far western blotting far western blotting Affinity blotting Affinity blotting tag enzyme assay tag visualisation by enzyme assay tag enzyme assay Zhang M., Zhou Y., Li T., Wang H., Cheng F., Zhou Y., Bi L., Zhang X.E. blj@sun5.ibp.ac.cn, x.zhang@wh.iov.cn Arch. Biochem. Biophys. (0003-9861) 2012 Only protein-protein interactions imex curation zhang-2012b-2 MutL associates with Escherichia coli RecA and inhibits its ATPase activity. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Zhang M., Zhou Y., Li T., Wang H., Cheng F., Zhou Y., Bi L., Zhang X.E. blj@sun5.ibp.ac.cn, x.zhang@wh.iov.cn Arch. Biochem. Biophys. (0003-9861) 2012 Only protein-protein interactions imex curation zhang-2012b-4 MutL associates with Escherichia coli RecA and inhibits its ATPase activity. in vitro In vitro electrophoresis electrophoretic mobility-based method electrophoresis predetermined predetermined participant predetermined Zhang M., Zhou Y., Li T., Wang H., Cheng F., Zhou Y., Bi L., Zhang X.E. blj@sun5.ibp.ac.cn, x.zhang@wh.iov.cn Arch. Biochem. Biophys. (0003-9861) 2012 Only protein-protein interactions imex curation mutl_ecoli DNA mismatch repair protein MutL mutL b4170 JW4128 protein protein ecoli Escherichia coli (strain K12) MPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQQQLETPLPLDDEPQPAPRSIPENRVAAGRNHFAEPAAREPVAPRYTPAPASGSRPAAPWPNAQPGYQKQQGEVYRQLLQTPAPMQKLKAPEPQEPALAANSQSFGRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQSDAQHVTIRAVPLPLRQQNLQILIPELIGYLAKQSVFEPGNIAQWIARNLMSEHAQWSMAQAITLLADVERLCPQLVKTPPGGLLQSVDLHPAIKALKDE 90mer_polyt single-stranded biotinylated 90mer-polyT ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) reca_ecoli Protein RecA recA lexB recH rnmB umuB tif zab b2699 Recombinase A JW2669 protein protein ecoli Escherichia coli (strain K12) MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF m13mp18 M13mp18ssDNA ss dna single stranded deoxyribonucleic acid ss DNA ss dna ecoli Escherichia coli (strain K12) 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) ssb_ecoli Single-stranded DNA-binding protein Helix-destabilizing protein ssb exrB lexC b4059 JW4020 protein protein ecoli Escherichia coli (strain K12) MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF 90mer-mutl-1 1322270 n/a 1322275 unspecified role unspecified role prey prey histag 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 1322276 unspecified role unspecified role bait bait direct interaction direct interaction false false false Figure 2 90mer-mutl-2 1322270 n/a 1322276 unspecified role unspecified role bait bait n/a 1322277 unspecified role unspecified role prey prey 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) direct interaction direct interaction false false false Figure 2A mutl-reca 1322270 n/a 1322277 unspecified role unspecified role unspecified role unspecified role histag 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 n/a 1322275 unspecified role unspecified role unspecified role unspecified role histag 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 direct interaction direct interaction false false false supplemental Fig. S1 adenosine-m13mp18-3 1322271 n/a 1322278 ancillary ancillary unspecified role unspecified role n/a 1322279 enzyme target enzyme target substrate substrate unspecified role unspecified role n/a 1322280 ancillary ancillary unspecified role unspecified role ecoli Escherichia coli (strain K12) n/a 1322277 enzyme enzyme unspecified role unspecified role histag 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) atpase reaction atpase reaction false false false Figure 4 adenosine-m13mp18-2 1322271 n/a 1322280 ancillary ancillary unspecified role unspecified role n/a 1322279 enzyme target enzyme target substrate substrate unspecified role unspecified role n/a 1322278 ancillary ancillary unspecified role unspecified role n/a 1322275 enzyme enzyme unspecified role unspecified role P23367:p.Glu29Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false histag 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) atpase reaction atpase reaction false false false Figure 4 adenosine-m13mp18-1 1322271 n/a 1322280 ancillary ancillary unspecified role unspecified role n/a 1322275 inhibitor inhibitor unspecified role unspecified role histag 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 1322279 enzyme target enzyme target substrate substrate unspecified role unspecified role n/a 1322277 enzyme enzyme unspecified role unspecified role histag 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 1322278 ancillary ancillary unspecified role unspecified role atpase reaction atpase reaction false false false Figure 4 To verify whether it was the ATPase activity of RecA which was inhibited by MutL, the MutL mutant L-E29A, which is completely inactive in ATP hydrolysis but still has a physical interaction with RecA was added to the reaction system. As was the case with wild type MutL, L-E29A also had an inhibitory effect on RecA’s ATPase activity. reca-mutl 1322272 n/a 1322277 unspecified role unspecified role bait bait nucl transformation nucleic acid transformation nucl transformation histag 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 sbp sbp sbp 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 1322275 unspecified role unspecified role prey prey nucl transformation nucleic acid transformation nucl transformation histag 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 1A reca-mutl-1 1322273 n/a 1322277 unspecified role unspecified role bait bait nucl transformation nucleic acid transformation nucl transformation gst tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1322275 unspecified role unspecified role prey prey nucl transformation nucleic acid transformation nucl transformation region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false histag 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) direct interaction direct interaction false false false Figure 1B 90mer-reca-2 1322274 n/a 1322276 unspecified role unspecified role neutral component neutral component tmr fluorophore fluorophore undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1322277 unspecified role unspecified role neutral component neutral component histag 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) direct interaction direct interaction false false false Figure 3