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/ haas-2007-1 The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress confocal microscopy confocal microscopy tag fluorescence tag visualisation by fluorescence tag fluorescence Haas TJ., Sliwinski MK., Martinez DE., Preuss M., Ebine K., Ueda T., Nielsen E., Odorizzi G., Otegui MS. Transgenic arabidopsis plants (ecotype Columbia) expressing tagged proteins were used in this study. otegui@wisc.edu Plant Cell (1040-4651) 2007 Only protein-protein interactions imex curation haas-2007-2 The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy tag visualisation tag visualisation Haas TJ., Sliwinski MK., Martinez DE., Preuss M., Ebine K., Ueda T., Nielsen E., Odorizzi G., Otegui MS. Transgenic arabidopsis plants (ecotype Columbia) expressing tagged proteins were used in this study. otegui@wisc.edu Plant Cell (1040-4651) 2007 Only protein-protein interactions imex curation haas-2007-3 The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. 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 nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Haas TJ., Sliwinski MK., Martinez DE., Preuss M., Ebine K., Ueda T., Nielsen E., Odorizzi G., Otegui MS. Transgenic arabidopsis plants (ecotype Columbia) expressing tagged proteins were used in this study. otegui@wisc.edu A cDNA library from etiolated Arabidopsis (ecotype Columbia) seedlings. Plant Cell (1040-4651) 2007 Only protein-protein interactions imex curation haas-2007-4 The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. in vitro In vitro pull down pull down predetermined predetermined participant predetermined Haas TJ., Sliwinski MK., Martinez DE., Preuss M., Ebine K., Ueda T., Nielsen E., Odorizzi G., Otegui MS. Transgenic arabidopsis plants (ecotype Columbia) expressing tagged proteins were used in this study. otegui@wisc.edu Plant Cell (1040-4651) 2007 Only protein-protein interactions imex curation haas-2007-5 The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. in vitro In vitro atpase assay atpase assay predetermined predetermined participant predetermined Haas TJ., Sliwinski MK., Martinez DE., Preuss M., Ebine K., Ueda T., Nielsen E., Odorizzi G., Otegui MS. Transgenic arabidopsis plants (ecotype Columbia) expressing tagged proteins were used in this study. otegui@wisc.edu Plant Cell (1040-4651) 2007 Only protein-protein interactions imex curation vps4_arath Protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 SKD1 Protein VACUOLAR PROTEIN SORTING 4 VPS4 F10A12.27 F15K20 At2g27600 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MYSNFKEQAIEYVKQAVHEDNAGNYNKAFPLYMNALEYFKTHLKYEKNPKIREAITQKFTEYLRRAEEIRAVLDEGGSGPGSNGDAAVATRPKTKPKDGEGGGKDGEDPEQSKLRAGLNSAIVREKPNIKWSDVAGLESAKQALQEAVILPVKFPQFFTGKRRPWRAFLLYGPPGTGKSYLAKAVATEADSTFFSVSSSDLVSKWMGESEKLVSNLFEMARESAPSIIFVDEIDSLCGTRGEGNESEASRRIKTELLVQMQGVGHNDEKVLVLAATNTPYALDQAIRRRFDKRIYIPLPEAKARQHMFKVHLGDTPHNLTEPDFEYLGQKTEGFSGSDVSVCVKDVLFEPVRKTQDAMFFFKSPDGTWMPCGPRHPGAIQTTMQDLATKGLAEKIIPPPITRTDFEKVLARQRPTVSKSDLDVHERFTQEFGEEG rabf1_arath Ras-related protein RABF1 RABF1 At3g54840 ARA-6 RAB5C Ras-related protein Ara-6 Ras-related protein Rab5C F28P10.180 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MGCASSLPDRNSGTLSGLSNSENAVPADAKNLRVKLVLLGDSGVGKSCIVLRFVRGQFDATSKVTVGASFLSQTIALQDSTTVKFEIWDTAGQERYSALAPLYYRGAGVAVIVYDITSPESFKKAQYWVKELQKHGSPDIVMALVGNKADLHEKREVPTEDGMELAEKNGMFFIETSAKTADNINQLFEEIGKRLPRPAPSS raf2a_arath Ras-related protein RABF2a RABF2A K17O22.15 At5g45130 RAB5A RHA1 Ras-related protein Rab5A Ras-related protein Rha1 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MASSGNKNINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDITNQASFERAKKWVQELQAQGNPNMVMALAGNKADLLDARKVSAEEAEIYAQENSLFFMETSAKTATNVKDIFYEIAKRLPRVQPAENPTGMVLPNGPGATAVSSSCCA raf2b_arath Ras-related protein RABF2b RABF2B ARA-7 RAB5B At4g19640 Ras-related protein Ara-7 Ras-related protein Rab5B F24J7.190 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MAAAGNKSINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLPRVQPTENPTGMVLPDRAMDRAVSSSCCA lip5_arath Protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5 LIP5 Protein EXTENSIN-LIKE VTA1 F10M23.90 At4g26750 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSNPNEPARALLPYLQRADELQKHEPLVAYYCRLYAMERGLKIPQSERTKTTNSILMSLINQLEKDKKSLTLSPDDNMHVEGFALSVFAKADKQDRAGRADLGTAKTFYAASIFFEILSQFGPVPPDIEQKHKYAAWKAADIRKAIKEGRKPTPGDPVDDDTDLSIPSSGPSGSYDHSASDTNTTSHHRTELDPPHDSNDDSSHHQFPEVPQHPLPPRFYDNPTNDYPADVPPPPPSSYPSNDHLPPPTGPSDSPYPHPYSHQPYHQDPPKHMPPPQNYSSHEPSPNSLPNFQSYPSFSESSLPSTSPHYPSHYQNPEPYYSSPHSAPAPSSTSFSSAPPPPPYSSNGRINIAPVLDPAPSSAQKYHYDSSYQPGPEKVAEALKAARFAVGALAFDEVSTAVEHLKKSLELLTNPSAGAGH 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) at2g27600-ara6 Colocalisation of SKD1 and ARA6 720621 N/A 720626 unspecified role unspecified role neutral component neutral component region green fluorescent protein gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 720627 unspecified role unspecified role neutral component neutral component c-terminal monomeric red fluorescent protein tag rfp tag red fluorescent protein tag red fluorescent protein RFP red fluorescent protein RFP rfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false colocalization colocalization false false false Figure 4A Partial colocalisation was observed in epidermal root cells. at2g27600-rha1 Colocalisation of SKD1 and RHA1 (RabF2a) 720621 N/A 720628 unspecified role unspecified role neutral component neutral component n-terminal enhanced yellow fluorescent protein yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 720626 unspecified role unspecified role neutral component neutral component region green fluorescent protein gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false colocalization colocalization false false false Figure 4C Partial colocalisation was observed in epidermal root cells. at2g27600-at4g19640 Colocalisation of SKD1 and RabF2b 720621 N/A 720629 unspecified role unspecified role neutral component neutral component c-terminal monomeric red fluorescent protein rfp tag red fluorescent protein tag red fluorescent protein RFP red fluorescent protein RFP rfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 720626 unspecified role unspecified role neutral component neutral component region green fluorescent protein gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false colocalization colocalization false false false Figure 4B Partial colocalisation was observed in epidermal root cells. at2g27600-ara6-1 Colocalisation of SKD1 and ARA6 720622 N/A 720627 unspecified role unspecified role neutral component neutral component N/A 720626 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false Figure 6D at2g27600-at4g19640- Colocalisation of SKD1 and RabF2b 720622 N/A 720629 unspecified role unspecified role neutral component neutral component N/A 720626 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false Figure 6F A weak cross reaction of the anti-body to Rab2a (P31582) was observed in this study. at2g27600-rha1-1 Colocalisation of SKD1 and RHA1 (RabF2a) 720622 N/A 720626 unspecified role unspecified role neutral component neutral component N/A 720628 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false Figure 6E A weak cross reaction of the anti-body was observed with protein Rab2b (Q9SN68) at2g27600-at4g26750 Interaction between SKD1 and Lip5 720623 N/A 720626 unspecified role unspecified role bait bait N/A 720630 unspecified role unspecified role prey prey physical association physical association false false false at2g27600-at4g26750- Interaction between SKD1 and Lip5 720624 N/A 720630 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) N/A 720626 unspecified role unspecified role bait bait region 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) direct interaction direct interaction false false false Figure 9 at2g27600-atp SKD1 displays ATPase activity 720625 N/A 720631 enzyme target enzyme target substrate substrate neutral component neutral component N/A 720626 enzyme enzyme neutral component neutral component region 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) atpase reaction atpase reaction false false false Figure 10A Lip5 proten (Q9SZ15) stimulated ATPase activity In the absence of LIP5, SKD1 hydrolyzes approximately 106 micro Moles of ATP per min/per mg,in the presence of recombinant LIP5, the hydrolysis rate shows a fourfold to fivefold increase.