DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ chen-2007b-1 Structural basis of the recognition of a methylated histone tail by JMJD2A. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Chen Z., Zang J., Kappler J., Hong X., Crawford F., Wang Q., Lan F., Jiang C., Whetstine J., Dai S., Hansen K., Shi Y., Zhang G. Chromatin - Epigenetic interactions resulting in chromatin modulation Demethylation of H3k9Me3 and H3k36Me3 studied by maldi-tof. zhangg@njc.org zhangg@njc.org. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2007 IMEx Only protein-protein interactions imex curation chen-2007b-2 Structural basis of the recognition of a methylated histone tail by JMJD2A. in vitro In vitro demethylase assay demethylase assay ms participant Identification by mass spectrometry ms participant Chen Z., Zang J., Kappler J., Hong X., Crawford F., Wang Q., Lan F., Jiang C., Whetstine J., Dai S., Hansen K., Shi Y., Zhang G. Chromatin - Epigenetic interactions resulting in chromatin modulation Demethylation of H3k9Me3 and H3k36Me3 studied by maldi-tof. zhangg@njc.org zhangg@njc.org. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2007 IMEx Only protein-protein interactions imex curation chen-2007b-3 Structural basis of the recognition of a methylated histone tail by JMJD2A. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Chen Z., Zang J., Kappler J., Hong X., Crawford F., Wang Q., Lan F., Jiang C., Whetstine J., Dai S., Hansen K., Shi Y., Zhang G. Chromatin - Epigenetic interactions resulting in chromatin modulation Demethylation of H3k9Me3 and H3k36Me3 studied by maldi-tof. zhangg@njc.org zhangg@njc.org. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2007 IMEx Only protein-protein interactions imex curation h31t_human Histone H3.1t H3-4 H3/g H3FT HIST3H3 Histone H3.4 protein protein human Homo sapiens Human MARTKQTARKSTGGKAPRKQLATKVARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLMREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCVIHAKRVTIMPKDIQLARRIRGERA kdm4a_human Lysine-specific demethylase 4A KDM4A JMJD2 KIAA0677 Jumonji domain-containing protein 2A JHDM3A [histone H3]-trimethyl-L-lysine(36) demethylase 4A [histone H3]-trimethyl-L-lysine(9) demethylase 4A JMJD2A JmjC domain-containing histone demethylation protein 3A protein protein human Homo sapiens Human MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESELPPRAGNEEECPEEDMEGVEDGEEGDLKTSLAKHRIGTKRHRVCLEIPQEVSQSELFPKEDLSSEQYEMTECPAALAPVRPTHSSVRQVEDGLTFPDYSDSTEVKFEELKNVKLEEEDEEEEQAAAALDLSVNPASVGGRLVFSGSKKKSSSSLGSGSSRDSISSDSETSEPLSCRAQGQTGVLTVHSYAKGDGRVTVGEPCTRKKGSAARSFSERELAEVADEYMFSLEENKKSKGRRQPLSKLPRHHPLVLQECVSDDETSEQLTPEEEAEETEAWAKPLSQLWQNRPPNFEAEKEFNETMAQQAPHCAVCMIFQTYHQVEFGGFNQNCGNASDLAPQKQRTKPLIPEMCFTSTGCSTDINLSTPYLEEDGTSILVSCKKCSVRVHASCYGVPPAKASEDWMCSRCSANALEEDCCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCIFCKKRRKRTAGCCVQCSHGRCPTAFHVSCAQAAGVMMQPDDWPFVVFITCFRHKIPNLERAKGALQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELPKRVKSRLSVASDMRFNEIFTEKEVKQEKKRQRVINSRYREDYIEPALYRAIME jhd3a-h3_pep-1 653154 N/A 653157 unspecified role unspecified role neutral component neutral component lys36 n6me1lys N6-methyl-L-lysine (2S)-2-amino-6-methylaminohexanoic acid MOD_RES N6-methyllysine N(zeta)-methyllysine N6-methyl-L-lysine N6-methylated L-lysine epsilon-methyllysine Methyl Methylation N-methyl Lysyl N6Me1Lys 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 653158 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false working 25.6%, free 27.6% 2.00 A Table S1, Figure 1 jhd3a-h3_pep-2 653154 N/A 653157 unspecified role unspecified role neutral component neutral component lys36 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation 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 Q16695:p.Ala48Lys mutation mutation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 653158 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false working 23.8%, free 26.3% 1.99 A Table 1, Figure 1 Peptide is Lys is position 48 of the protein, whereas UniProt has Ala at this position. jhd3a-h3_pep-3 653155 N/A 653157 unspecified role unspecified role neutral component neutral component lys36 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation 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 653158 unspecified role unspecified role neutral component neutral component O75164:p.Asn86Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Gln88Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Asp135Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Tyr175Phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Tyr177Phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Lys241Leu mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Tyr177Leu mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Lys241Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Val mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Asp mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Ile mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) demethylation demethylation reaction demethylation false false false 2 Mutagenesis data and activity assays suggest residues Q86, N88, D135, and Y175 are involved in the interaction with the peptide, whereas residues Y177, N290, S288, and T289 are involved in methyl group binding. K241 is proposed to recruit the O2 molecule into the catalytic center. jhd3a-h3_pep-4 653155 N/A 653157 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 lys9 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 653158 unspecified role unspecified role neutral component neutral component O75164:p.Asn86Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Gln88Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Asp135Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Tyr175Phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Tyr177Phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false O75164:p.Lys241Leu mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Tyr177Leu mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Lys241Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Val mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Asp mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false O75164:p.Asn290Ile mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) demethylation demethylation reaction demethylation false false false 2 Mutagenesis data and activity assays suggest residues Q86, N88, D135, and Y175 are involved in the interaction with the peptide, whereas residues Y177, N290, S288, and T289 are involved in methyl group binding. K241 is proposed to recruit the O2 molecule into the catalytic center. jhd3a-h3_pep-5 653156 N/A 653157 unspecified role unspecified role bait bait lys36 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation 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 653158 unspecified role unspecified role prey prey 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 2C jhd3a-h3_pep-6 653156 N/A 653157 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false lys9 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 653158 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false O75164:p.[Gly133Ala;Gly138Ala] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false O75164:p.[Gly165Ala;Gly170Ala] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2D