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/ froese-2010-1 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Froese DS., Kochan G., Muniz JR., Wu X., Gileadi C., Ugochukwu E., Krysztofinska E., Gravel RA., Oppermann U., Yue WW. Rare diseases - Interactions investigated in the context of Rare genetic disease udo.oppermann@sgc.ox.ac.uk,wyatt.yue@sgc.ox.ac.uk The Journal of biological chemistry 2010 Only protein-protein interactions imex curation imex curation froese-2010-2 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Froese DS., Kochan G., Muniz JR., Wu X., Gileadi C., Ugochukwu E., Krysztofinska E., Gravel RA., Oppermann U., Yue WW. Rare diseases - Interactions investigated in the context of Rare genetic disease MMAA construct used for molecular sieving is N-terminally truncated. The authors state the range is 73-424; however we have only one sequence of MMAA in UniProt, which is of 418 aa length. So the range is considered as 73-418 udo.oppermann@sgc.ox.ac.uk,wyatt.yue@sgc.ox.ac.uk The Journal of biological chemistry 2010 Only protein-protein interactions imex curation imex curation froese-2010-3 in vitro In vitro gtpase assay gtpase assay GTPase gtp hydrolisis gtp hydrolisis GTPase predetermined predetermined participant predetermined Froese DS., Kochan G., Muniz JR., Wu X., Gileadi C., Ugochukwu E., Krysztofinska E., Gravel RA., Oppermann U., Yue WW. Rare diseases - Interactions investigated in the context of Rare genetic disease MMAA construct used for molecular sieving is N-terminally truncated. The authors state the range is 73-424; however we have only one sequence of MMAA in UniProt, which is of 418 aa length. So the range is considered as 73-418 udo.oppermann@sgc.ox.ac.uk,wyatt.yue@sgc.ox.ac.uk The Journal of biological chemistry 2010 Only protein-protein interactions imex curation imex curation froese-2010-4 human-hep_g2 Homo sapiens hepatocellular carcinoma (HCC) cells (p53-wt). hep_g2 human hepatocellular carcinoma (HCC) cells (p53-wt). anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Froese DS., Kochan G., Muniz JR., Wu X., Gileadi C., Ugochukwu E., Krysztofinska E., Gravel RA., Oppermann U., Yue WW. Rare diseases - Interactions investigated in the context of Rare genetic disease udo.oppermann@sgc.ox.ac.uk,wyatt.yue@sgc.ox.ac.uk The Journal of biological chemistry 2010 Only protein-protein interactions imex curation imex curation cobamamide cobamamide (5,6-Dimethylbenzimidazolyl)cobamide coenzyme (5,6-dimethylbenzimidazolyl)cobamide coenzyme 5'-Deoxy-5'-adenosyl vitamin B12 5'-Deoxy-5'-adenosyl-5,6-dimethylbenzimidazolylcobamide 5'-Deoxy-5'-adenosylcobalamin 5'-deoxyadenosyl vitamin B12 5'-deoxyadenosyl-5,6-dimethylbenzimidazolylcobamide 5'-deoxyadenosylcobalamin 5,6-Dimethylbenzimidazolyl-5-deoxyadenosyl-cobamide 5,6-Dimethylbenzimidazolyl-Co-5'-deoxy-5'-adenosylcobamide adenosylcob(III)alamin Adenosylcob(III)alamin Adenosylcobalamin adenosylcobalamin AdoCbl alpha-(5,6-Dimethylbenzimidazolyl)cobamide coenzyme Calomide Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-adenosylcobamide Cobalamin coenzyme cobamamid cobamamida Cobamamide cobamamide cobamamidum cobamide coenzyme coenzyme B-12 Coenzyme B12 DBC coenzyme Deoxyadenosylcobalamin Dibencozide DMBC coenzyme Funacomide Vitamin B12 coenzyme Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-(5'-deoxy-5'-adenosyl)cobamide small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) muta_human Methylmalonyl-CoA mutase, mitochondrial MMUT MUT Methylmalonyl-CoA isomerase protein protein human Homo sapiens Human MLRAKNQLFLLSPHYLRQVKESSGSRLIQQRLLHQQQPLHPEWAALAKKQLKGKNPEDLIWHTPEGISIKPLYSKRDTMDLPEELPGVKPFTRGPYPTMYTFRPWTIRQYAGFSTVEESNKFYKDNIKAGQQGLSVAFDLATHRGYDSDNPRVRGDVGMAGVAIDTVEDTKILFDGIPLEKMSVSMTMNGAVIPVLANFIVTGEEQGVPKEKLTGTIQNDILKEFMVRNTYIFPPEPSMKIIADIFEYTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGLEYSRTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKMRAGRRLWAHLIEKMFQPKNSKSLLLRAHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSLHTNSFDEALGLPTVKSARIARNTQIIIQEESGIPKVADPWGGSYMMECLTNDVYDAALKLINEIEEMGGMAKAVAEGIPKLRIEECAARRQARIDSGSEVIVGVNKYQLEKEDAVEVLAIDNTSVRNRQIEKLKKIKSSRDQALAERCLAALTECAASGDGNILALAVDASRARCTVGEITDALKKVFGEHKANDRMVSGAYRQEFGESKEITSAIKRVHKFMEREGRRPRLLVAKMGQDGHDRGAKVIATGFADLGFDVDIGPLFQTPREVAQQAVDADVHAVGISTLAAGHKTLVPELIKELNSLGRPDILVMCGGVIPPQDYEFLFEVGVSNVFGPGTRIPKAAVQVLDDIEKCLEKKQQSV malonyl-coa malonyl-CoA Coenzyme A, S-(hydrogen propanedioate) Malonyl coenzyme A Malonyl-CoA S-(Hydrogen malonyl)coenzyme A 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(3-carboxyacetyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) mmaa_human Methylmalonic aciduria type A protein, mitochondrial MMAA protein protein human Homo sapiens Human MPMLLPHPHQHFLKGLLRAPFRCYHFIFHSSTHLGSGIPCAQPFNSLGLHCTKWMLLSDGLKRKLCVQTTLKDHTEGLSDKEQRFVDKLYTGLIQGQRACLAEAITLVESTHSRKKELAQVLLQKVLLYHREQEQSNKGKPLAFRVGLSGPPGAGKSTFIEYFGKMLTERGHKLSVLAVDPSSCTSGGSLLGDKTRMTELSRDMNAYIRPSPTRGTLGGVTRTTNEAILLCEGAGYDIILIETVGVGQSEFAVADMVDMFVLLLPPAGGDELQGIKRGIIEMADLVAVTKSDGDLIVPARRIQAEYVSALKLLRKRSQVWKPKVIRISARSGEGISEMWDKMKDFQDLMLASGELTAKRRKQQKVWMWNLIQESVLEHFRTHPTVREQIPLLEQKVLIGALSPGLAADFLLKAFKSRD guanosine 5'-[beta,gamma-imido]triphosphate guanosine 5'-[beta,gamma-imido]triphosphate 5'-Guanylic acid, monoanhydride with imidodiphosphoric acid 5'-guanylylimidodiphosphate GMP-PNP GMP-Pnp Gpp(NH)-p Gpp(NH)p Guanylyl imidodiphosphate 5'-O-(hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl)guanosine small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) gtp guanosine triphosphate - GTP 5'-GTP GTP Guanosine 5'-triphosphate guanosine 5'-triphosphoric acid guanosine triphosphate GUANOSINE-5'-TRIPHOSPHATE H4gtp guanosine 5'-(tetrahydrogen triphosphate) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) InChI=1/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1/f/h14,19-20,22,24H,11H2 cobamamide-mmut-1 3649528 N/A 3649532 cofactor cofactor coenzyme neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 3649533 unspecified role unspecified role neutral component neutral component purified purified 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) Stoichiometry: 2.0 direct interaction direct interaction false false false TABLE 1 1.95Å Rwork:0.158 Rfree:0.199 cobamamide-mmut-2 3649528 N/A 3649534 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 2.0 N/A 3649532 cofactor cofactor coenzyme neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 2.0 N/A 3649533 unspecified role unspecified role neutral component neutral component purified purified 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) Stoichiometry: 2.0 physical association physical association false false false TABLE 1 1.95Å Rwork:0.161 Rfree:0.201 mmaa-1 3649528 N/A 3649535 unspecified role unspecified role neutral component neutral component purified purified 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) Stoichiometry: 2.0 direct interaction direct interaction false false false Table 1 2.64Å Rwork: 0.182 Rfree: 0.222 mmut-1 3649528 N/A 3649533 unspecified role unspecified role neutral component neutral component purified purified 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) Stoichiometry: 2.0 direct interaction direct interaction false false false Table 1 2.6Å Rwork: 0.217 Rfree: 0.243 guanosine 5'_[beta,gamma_imido]triphosphate-mmaa-1 3649529 N/A 3649535 unspecified role unspecified role neutral component neutral component purified purified n-terminal region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q8IVH4:p.Gly188Arg mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 3649533 unspecified role unspecified role neutral component neutral component purified purified c-terminal region 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 c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range 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) Stoichiometry: 1.0 N/A 3649536 cofactor cofactor coenzyme neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 physical association physical association false false false Fig. S2, 5b mmaa-4 3649529 N/A 3649535 unspecified role unspecified role neutral component neutral component purified purified n-terminal region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q8IVH4:p.Gly188Arg mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. S2 mmut-2 3649529 N/A 3649533 unspecified role unspecified role neutral component neutral component purified purified c-terminal region 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 c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range 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) Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. S2 gtp-mmaa-3 3649530 N/A 3649537 enzyme target enzyme target substrate substrate neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) N/A 3649535 enzyme enzyme neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q8IVH4:p.Gly188Arg mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3649533 stimulator stimulator neutral component neutral component purified purified c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range 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) gtpase reaction gtpase reaction false false false 3649530 3649530 TABLE 2, FIGURE 5a gtp-mmaa-4 3649530 N/A 3649535 enzyme enzyme neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminal region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q8IVH4:p.Gly188Arg mutation increasing rate mutation increasing interaction rate mutation increasing rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3649537 enzyme target enzyme target substrate substrate neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) gtpase reaction gtpase reaction false false false 3649530 3649530 TABLE 2, FIGURE 5a cobamamide-gtp-1 3649530 N/A 3649532 cofactor cofactor coenzyme neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) N/A 3649535 enzyme enzyme neutral component neutral component purified purified 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) N/A 3649533 stimulator stimulator neutral component neutral component purified purified c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range 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) N/A 3649537 enzyme target enzyme target substrate substrate neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) gtpase reaction gtpase reaction false false false 3649530 3649530 TABLE 2, FIGURE 5a mmaa-mmut-3 3649531 N/A 3649533 unspecified role unspecified role prey prey living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3649535 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell c-terminal region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false Q8IVH4:p.Gly188Arg mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig. 5c