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/ Proline isomerization of histone H3 regulates lysine methylation and gene expression. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell (0092-8674) 2006 imex curation Nelson CJ., Santos-Rosa H., Kouzarides T. Chromatin - Epigenetic interactions resulting in chromatin modulation t.kouzarides@gurdon.cam.ac.uk 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions 7 in vitro In vitro pull down pull down predetermined predetermined participant predetermined Nelson CJ., Santos-Rosa H., Kouzarides T. Chromatin - Epigenetic interactions resulting in chromatin modulation t.kouzarides@gurdon.cam.ac.uk Accepted 2006-OCT-13 by DAVET. Cell (0092-8674) 2006 Only protein-protein interactions 7 imex curation Proline isomerization of histone H3 regulates lysine methylation and gene expression. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell (0092-8674) 2006 imex curation Nelson CJ., Santos-Rosa H., Kouzarides T. Chromatin - Epigenetic interactions resulting in chromatin modulation t.kouzarides@gurdon.cam.ac.uk 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions 7 in vitro In vitro enzymatic study enzymatic study predetermined predetermined participant predetermined Nelson CJ., Santos-Rosa H., Kouzarides T. Chromatin - Epigenetic interactions resulting in chromatin modulation In a protease-coupled proline isomerization assay (Fischer et al., 1984a, 1984b), H3 and H4 peptides were designed that contained each of the candidate prolines followed by a phenyalanine (F) and paranitroanaline (pNA) group. Chymotrypsin exclusively cleaves these peptides in the trans-proline conformation (Fischer et al., 1984a) and does so with kinetics much faster than the isomerization of proline. Thus, the cis-trans conversion rate can be measured as chymotrypsin dependent release of pNA, which is measured spectrophotometrically at 390 nm. t.kouzarides@gurdon.cam.ac.uk Accepted 2006-OCT-13 by DAVET. 24-JAN-2007: Contacted by JYOTI. Cell (0092-8674) 2006 Only protein-protein interactions 7 imex curation Proline isomerization of histone H3 regulates lysine methylation and gene expression. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell (0092-8674) 2006 imex curation Nelson CJ., Santos-Rosa H., Kouzarides T. Chromatin - Epigenetic interactions resulting in chromatin modulation t.kouzarides@gurdon.cam.ac.uk 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions 7 in vitro In vitro enzymatic study enzymatic study predetermined predetermined participant predetermined Nelson CJ., Santos-Rosa H., Kouzarides T. Chromatin - Epigenetic interactions resulting in chromatin modulation Synthetic peptides representing amino acids 29�43 of histone H3 were incubated with recombinant Set2 and 3H-S-adenosyl methionine and methylation monitored by incorporation of 3H into peptides. At the indicated times aliquots were removed and 3H incorporation determined by PAGE, followed by fluorography. t.kouzarides@gurdon.cam.ac.uk Accepted 2006-OCT-13 by DAVET. 24-JAN-2007: Contacted by JYOTI. Cell (0092-8674) 2006 Only protein-protein interactions 7 imex curation h4_yeast Histone H4 N2752 YBR0122 YBR009C YNL030W HHF1 HHF2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 69B7D1F89E62DE41 69B7D1F89E62DE41 set2_yeast Histone-lysine N-methyltransferase, H3 lysine-36 specific SET2 EZL1 YJL168C J0520 KMT3 SET domain-containing protein 2 Lysine N-methyltransferase 3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSKNQSVSASEDEKEILNNNAEGHKPQRLFDQEPDLTEEALTKFENLDDCIYANKRIGTFKNNDFMECDCYEEFSDGVNHACDEDSDCINRLTLIECVNDLCSSCGNDCQNQRFQKKQYAPIAIFKTKHKGYGVRAEQDIEANQFIYEYKGEVIEEMEFRDRLIDYDQRHFKHFYFMMLQNGEFIDATIKGSLARFCNHSCSPNAYVNKWVVKDKLRMGIFAQRKILKGEEITFDYNVDRYGAQAQKCYCEEPNCIGFLGGKTQTDAASLLPQNIADALGVTVSMEKKWLKLKKLSGEPIIKNENENINIEFLQSLEVQPIDSPVDVTKIMSVLLQQDNKIIASKLLKRLFTIDDDSLRHQAIKLHGYTCFSKMLKLFITEQPQVDGKGNETEEDDIKFIKGILDFLLELPKTTRNGIESSQIDNVVKTLPAKFPFLKPNCDELLEKWSKFETYKRITKKDINVAASKMIDLRRVRLPPGWEIIHENGRPLYYNAEQKTKLHYPPSGSSKVFSSRSNTQVNSPSSSGIPKTPGALDSKKHKLSDEEYERKKQKRLEYERIALERAKQEELESLKQKLKLENERKSVLEDIIAEANKQKELQKEEAKKLVEAKEAKRLKRKTVSQSQRLEHNWNKFFASFVPNLIKKNPQSKQFDHENIKQCAKDIVKILTTKELKKDSSRAPPDDLTKGKRHKVKEFINSYMDKIILKKKQKKALALSSASTRMSSPPPSTSS 05436B181E88EFF5 05436B181E88EFF5 h3_yeast Histone H3 SIN2 YNL031C N2749 HHT1 YBR010W YBR0201 HHT2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS A6115FEB480AC67A A6115FEB480AC67A fkbp4_yeast FK506-binding protein 4 FPR4 YLR449W L9324.3 Peptidyl-prolyl cis-trans isomerase Rotamase Histone proline isomerase protein protein yeast Saccharomyces cerevisiae Baker's yeast MSDMLPLATYSLNVEPYSPTPALNFKIPVTIRITMAAIDPEPFDDDKKPSTLRIIKRNPELTRGEYYNQDNNDGLEEDESESEQEADVPKRSVKSKKGKAVEQSESEDSEDENEIDDEFEECVLLTLSPKGQYQQALDITIAPEEDVQFVVTGSYTISLTGNYVKHPFDNSSDSDEDEEDYYSDEESSNGEEEEEEEEEDDEELSSGDDDLDDLVDASDIESRLDELVKKDEKKKNNKKDSKRKHEEDEEESAKPAEKKQTTKKDKKAEKVKDSEESKPKPKTKLLEGGIIIEDRVTGKGPHAKKGTRVGMRYVGKLKNGKVFDKNTKGKPFVFKLGQGEVIKGWDIGVAGMAVGGERRIVIPAPYAYGKQALPGIPANSELTFDVKLVSMK CF90C6714F04572E CF90C6714F04572E fpr4-hht1 1 6 unspecified role unspecified role prey prey n-terminal required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobb Escherichia coli (strain B / BL21) 7 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 n-terminal nucleolin-like (NL) domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association The binding of Fpr4 to H3 takes place via the H3 amino terminus, as recombinant histone H3 lacking the amino-terminal 21 amino acids (H3 D1�21), is not recovered by GST-Fpr4 (Figure 1B). The sequence of Fpr4 indicates the presence of two distinct domains: a carboxyl-terminal peptidyl-proline isomerase (PPI) domain (aa 280�411), which is common to all four members of the FKBP family and an amino terminal highly charged nucleolin-like (NL) domain (aa 1�280), which is present only in Fpr3 and Fpr4 (Figure 1C). To establish which one of these domains is responsible for interaction between Fpr4 and histones, the isomerase (PPI) and nucleolin-like (NL) domains were expressed separately and assayed for binding to recombinant histones (Figure 1D). Fpr4�s NL domain (GST-Fpr4[NL]) recovered histone H3 and H4 with comparable efficiency to fulllength Fpr4 (GST-Fpr4), 1 A-D The nucleolin domain of Fpr4 is sufficient to interact with histone H3 and the N-terminal 21 residues of histone H3 are required for Fpr4 interaction. fpr4-hhf1 1 7 unspecified role unspecified role bait bait n-terminal nucleolin-like (NL) domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain 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 ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role prey prey ecobb Escherichia coli (strain B / BL21) physical association physical association Fpr4�s NL domain (GST-Fpr4[NL]) recovered histone H3 and H4 with comparable efficiency to fulllength Fpr4 (GST-Fpr4), 1 A, C, D The nucleolin domain of Fpr4 is sufficient to interact with histone H4. hht1-fpr4 1 6 unspecified role unspecified role bait bait region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 7 unspecified role unspecified role prey prey 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 n-terminal nucleolin-like (NL) domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association 1 E, F Only an affinity resin made of H3(1�16) peptide was able to recover the Fpr4(NL) domain hhf1-fpr4 1 7 unspecified role unspecified role prey prey n-terminal nucleolin-like (NL) domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain 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 ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role bait bait n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association 1 E, F amino acids 1�13 of H4 are bound by the NL domain, fpr4-hht1-1 2 6 enzyme target enzyme target substrate substrate unspecified role unspecified role region Peptide H3-P30 (RKSAPF-pNA) sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain c-terminal paranitroanaline (pNA) tag tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range chemical synthesis Chemical synthesis (Chemical synthesis) 7 enzyme enzyme unspecified role unspecified role 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 Q06205:p.Phe323Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain F A Wed May 02 17:22:06 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'phe323ala' Tue Jun 30 18:27:31 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Phe323Ala' ecoli Escherichia coli (strain K12) enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction Using this assay, Fpr4 was seen to have cis to trans isomerase activity on P30 and P38 of H3 but minimal activity toward H3P16 or H4P32 2 The H3 synthetic peptide has a Phe added after Pro30. Fpr4 has cis to trans activity on pro30 of histone H3. fpr4-hht1-2 2 7 enzyme enzyme unspecified role unspecified role 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 Q06205:p.Phe323Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain F A Wed May 02 14:36:10 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'phe323ala' Tue Jun 30 16:15:38 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Phe323Ala' ecoli Escherichia coli (strain K12) 6 enzyme target enzyme target substrate substrate unspecified role unspecified role region Peptide H3-P38 (GVKKPF-pNA) sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain c-terminal paranitroanaline (pNA) tag tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range chemical synthesis Chemical synthesis (Chemical synthesis) enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction Using this assay, Fpr4 was seen to have cis to trans isomerase activity on P30 and P38 of H3 but minimal activity toward H3P16 or H4P32 2 The H3 synthetic peptide has a Phe added after Pro38. Methylation of K36 in the peptide H3-P38 eliminates the ability of Fpr4 to isomerize this peptide in this assay. Fpr4 has cis to trans activity on pro38 of histone H4. set2-hht1 3 5 enzyme enzyme unspecified role unspecified role ecoli Escherichia coli (strain K12) 6 enzyme target enzyme target substrate substrate unspecified role unspecified role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction methylation of unmodified peptide occurs rapidly in vitro as labeled peptide is detected as early as 2 min after Set2 addition 3 A The addition of recombinant Fpr4 slows the rate of methylation by Set2. The Fpr4 isomerase activity causes this inhibition as addition of a catalytically inactive Fpr4 has no influence on the kinetics of methylation. Set2 methylates histone H3.