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/ yu-2011b-2 Substrate specificity of lymphoid-specific tyrosine phosphatase (Lyp) and identification of Src kinase-associated protein of 55 kDa homolog (SKAP-HOM) as a Lyp substrate. in vitro In vitro phosphatase assay phosphatase assay predetermined predetermined participant predetermined Yu X., Chen M., Zhang S., Yu Z.H., Sun J.P., Wang L., Liu S., Imasaki T., Takagi Y., Zhang Z.Y. IBD - Inflammatory bowel disease Expression and purification of the Lyp/PTPN22 construct is described in PMID:18056643. zyzhang@iupui.edu J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease yu-2011b-4 Substrate specificity of lymphoid-specific tyrosine phosphatase (Lyp) and identification of Src kinase-associated protein of 55 kDa homolog (SKAP-HOM) as a Lyp substrate. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Yu X., Chen M., Zhang S., Yu Z.H., Sun J.P., Wang L., Liu S., Imasaki T., Takagi Y., Zhang Z.Y. IBD - Inflammatory bowel disease zyzhang@iupui.edu J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease yu-2011b-1 Substrate specificity of lymphoid-specific tyrosine phosphatase (Lyp) and identification of Src kinase-associated protein of 55 kDa homolog (SKAP-HOM) as a Lyp substrate. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Yu X., Chen M., Zhang S., Yu Z.H., Sun J.P., Wang L., Liu S., Imasaki T., Takagi Y., Zhang Z.Y. IBD - Inflammatory bowel disease Expression and purification of the Lyp/PTPN22 construct is described in PMID:18056643. zyzhang@iupui.edu J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease yu-2011b-3 Substrate specificity of lymphoid-specific tyrosine phosphatase (Lyp) and identification of Src kinase-associated protein of 55 kDa homolog (SKAP-HOM) as a Lyp substrate. human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Yu X., Chen M., Zhang S., Yu Z.H., Sun J.P., Wang L., Liu S., Imasaki T., Takagi Y., Zhang Z.Y. IBD - Inflammatory bowel disease zyzhang@iupui.edu J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease ptn22_human Tyrosine-protein phosphatase non-receptor type 22 PTPN22 PTPN8 Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP Lymphoid phosphatase PEST-domain phosphatase protein protein human Homo sapiens Human MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNSETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGTESQAKHCIPEKNHTLQADSYSPNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSEISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKWQTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKSTPFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDSKHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSWPPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSYYNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEEAGEFSPNVPKSLSSAVKVKIGTSLEWGGTSEPKKFDDSVILRPSKSVKLRSPKSELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLKTPGKSFTRSKSLKILRNMKKSICNSCPPNKPAESVQSNNSSSFLNFGFANRFSKPKGPRNPPPTWNI skap2_human Src kinase-associated phosphoprotein 2 SKAP2 PRAP RA70 SAPS SCAP2 SKAP55R Src family-associated phosphoprotein 2 Src kinase-associated phosphoprotein 55-related protein SKAP55 homolog Src-associated adapter protein with PH and SH3 domains Pyk2/RAFTK-associated protein Retinoic acid-induced protein 70 protein protein human Homo sapiens Human MPNPSSTSSPYPLPEEIRNLLADVETFVADILKGENLSKKAKEKRESLIKKIKDVKSIYLQEFQDKGDAEDGEEYDDPFAGPPDTISLASERYDKDDEAPSDGAQFPPIAAQDLPFVLKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYSVRMNNTLRKDGKKDCCFEISAPDKRIYQFTAASPKDAEEWVQQLKFVLQDMESDIIPEDYDERGELYDDVDHPLPISNPLTSSQPIDDEIYEELPEEEEDSAPVKVEEQRKMSQDSVHHTSGDKSTDYANFYQGLWDCTGAFSDELSFKRGDVIYILSKEYNRYGWWVGEMKGAIGLVPKAYIMEMYDI lck_human Tyrosine-protein kinase Lck Protein YT16 Proto-oncogene Lck T cell-specific protein-tyrosine kinase LCK Lymphocyte cell-specific protein-tyrosine kinase p56-LCK Leukocyte C-terminal Src kinase protein protein human Homo sapiens Human MGCGCSSHPEDDWMENIDVCENCHYPIVPLDGKGTLLIRNGSEVRDPLVTYEGSNPPASPLQDNLVIALHSYEPSHDGDLGFEKGEQLRILEQSGEWWKAQSLTTGQEGFIPFNFVAKANSLEPEPWFFKNLSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQNQGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNASDGLCTRLSRPCQTQKPQKPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMSPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTATEGQYQPQP ptn22_substrate_peptide-1 Tyrosine-protein phosphatase non-receptor type 22 (PTN22) consensus substrate peptide-1 peptide peptide polypeptide oligopeptide oligopeptide polypeptide chemical synthesis Chemical synthesis (Chemical synthesis) YGEEYDDLY ptn22_substrate_peptide-2 Tyrosine-protein phosphatase non-receptor type 22 (PTN22) consensus substrate peptide-2 peptide peptide polypeptide oligopeptide oligopeptide polypeptide chemical synthesis Chemical synthesis (Chemical synthesis) YGYEYDDEY skap2_mouse Src kinase-associated phosphoprotein 2 Src family-associated phosphoprotein 2 Src kinase-associated phosphoprotein 55-related protein SKAP55 homolog Src-associated adapter protein with PH and SH3 domains Pyk2/RAFTK-associated protein Skap2 Prap Saps Ra70 Scap2 Skap55r protein protein mouse Mus musculus Mouse MPNPSCTSSPGPLPEEIRNLLADVETFVADTLKGENLSKKAKEKRESLIKKIKDVKSVYLQEFQDKGDAEDGDEYDDPFAGPADTISLASERYDKDDDGPSDGNQFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLGSDVIPEDDEERGELYDDVDHPAAVSSPQRSQPIDDEIYEELPEEEEDTASVKMDEQGKGSRDSVHHTSGDKSTDYANFYQGLWDCTGALSDELSFKRGDVIYILSKEYNRYGWWVGEMKGAIGLVPKAYLMEMYDI ptpn22-skap2-1 1571410 n/a 1571414 enzyme enzyme neutral component neutral component n-terminus 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 tyr_pase_rcpt/non-rcpt sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1571415 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false phosphotyr-75 optyr O4'-phospho-L-tyrosine (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid MOD_RES Phosphotyrosine O4-phosphotyrosine tyrosine phosphate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4'-phosphorylated L-tyrosine OPTyr Phospho Phospho Tyrosinyl Phosphorylation phosphorylationy certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) 1571425 1571423 dephosphorylation dephosphorylation reaction dephosphorylation false false false Table 1 Q9Y2R2 is required for dephosphorylation of O75563 Temp = 25C, pH = 7 kcat/Km = 40 +/- 0.3 x 10E-5 M-1 s-1 lck-ptpn22 1571410 n/a 1571416 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false phosphotyr-394 optyr O4'-phospho-L-tyrosine (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid MOD_RES Phosphotyrosine O4-phosphotyrosine tyrosine phosphate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4'-phosphorylated L-tyrosine OPTyr Phospho Phospho Tyrosinyl Phosphorylation phosphorylationy certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1571414 enzyme enzyme neutral component neutral component n-terminus 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 tyr_pase_rcpt/non-rcpt sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) 1571433 1571429 dephosphorylation dephosphorylation reaction dephosphorylation false false false Table 1 Q9Y2R2 is required for dephosphorylation of P06239 Temp = 25C, pH = 7 kcat/Km = 6.2 +/- 0.1 x 10E-5 M-1 s-1 ptn22-ptpn22 1571410 n/a 1571417 enzyme target enzyme target substrate substrate neutral component neutral component phosphotyr-5 optyr O4'-phospho-L-tyrosine (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid MOD_RES Phosphotyrosine O4-phosphotyrosine tyrosine phosphate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4'-phosphorylated L-tyrosine OPTyr Phospho Phospho Tyrosinyl Phosphorylation phosphorylationy certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1571414 enzyme enzyme neutral component neutral component n-terminus 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 tyr_pase_rcpt/non-rcpt sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) 1571440 1571437 dephosphorylation dephosphorylation reaction dephosphorylation false false false Table 1 kcat/Km = 46 +/- 0.5 x 10E-5 M-1 s-1 Temp = 25C, pH = 7 ptn22-ptpn22-1 1571410 n/a 1571414 enzyme enzyme neutral component neutral component n-terminus 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 tyr_pase_rcpt/non-rcpt sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1571418 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false phosphotyr-5 optyr O4'-phospho-L-tyrosine (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid MOD_RES Phosphotyrosine O4-phosphotyrosine tyrosine phosphate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4'-phosphorylated L-tyrosine OPTyr Phospho Phospho Tyrosinyl Phosphorylation phosphorylationy certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) 1571446 1571444 dephosphorylation dephosphorylation reaction dephosphorylation false false false Table 1 kcat/Km = 21 +/- 0.1 x 10E-5 M-1 s-1 Temp = 25C, pH = 7 ptpn22-skap2-2 1571411 n/a 1571419 unspecified role unspecified role prey prey possible phosphotyr optyr O4'-phospho-L-tyrosine (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid MOD_RES Phosphotyrosine O4-phosphotyrosine tyrosine phosphate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4'-phosphorylated L-tyrosine OPTyr Phospho Phospho Tyrosinyl Phosphorylation phosphorylationy undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-raw264_7 Mus musculus monocyte macrophage cell line RAW264 raw264_7 Mouse monocyte macrophage cellline RAW264.7 n/a 1571414 unspecified role unspecified role bait bait n-terminus 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 Q9Y2R2:p.Asp195Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) physical association physical association false false false Fig. 2a The wild type Lyp does not interact with SKAP-HOM. ptpn22-skap2-3 1571411 n/a 1571414 unspecified role unspecified role bait bait Q9Y2R2:p.Cys227Ser mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false n-terminus 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 ecobb Escherichia coli (strain B / BL21) n/a 1571419 unspecified role unspecified role prey prey mouse-raw264_7 Mus musculus monocyte macrophage cell line RAW264 raw264_7 Mouse monocyte macrophage cellline RAW264.7 physical association physical association false false false Fig. 2a The wild type Lyp does not interact with SKAP-HOM. ptpn22-skap2 1571412 n/a 1571415 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 false phosphotyr-75 optyr O4'-phospho-L-tyrosine (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid MOD_RES Phosphotyrosine O4-phosphotyrosine tyrosine phosphate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4'-phosphorylated L-tyrosine OPTyr Phospho Phospho Tyrosinyl Phosphorylation phosphorylationy certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 4.0 n/a 1571414 unspecified role unspecified role neutral component neutral component n-terminus 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 catalytic_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) Stoichiometry: 4.0 1571465 1571461 direct interaction direct interaction false false false Table 2 2.90A working 16.4%, free 22.3% skap2-ptpn22 1571413 n/a 1571414 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Q9Y2R2:p.Asp195Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false n/a 1571415 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 2b The wild type Lyp does not interact with SKAP-HOM.