Sandbox Reserved 897: Difference between revisions

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===Methyl-lysine reader===

PWWP domains are one of the epigenetic regulators which recognize specific lysine residues that are methylated. Even though there is no detailed research on 3pfs, it may be assumed to have similar function with BRPF1 PWWP domain which is shown to have methylated histone binding activity.<ref>Vezzoli A, Bonadies N, Allen MD, Freund SM, Santiveri CM, Kvinlaug BT, Huntly BJ, Göttgens B, Bycroft M. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nature structural & molecular biology. 2010 May;17(5):617-9.</ref> With a high-throughput mass spectrometry screening, ~~this motif~~ is suggested as an essential ~~motif~~ of histone 3 lysine 36 trimethylation binding.<ref>Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010 Sep 17;142(6):967-80.</ref> The β-strands and Pro-Trp-Trp-Pro motif form hydrophobic cavity, which is the binding site of methylated lysines.<ref>Rona GB, Eleutherio EC, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophysical reviews. 2016 Mar 1;8(1):63-74.</ref> Since the aromatic cage is a common structure in the Royal family, it can be a common tool for methylated lysine binding.<ref>Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J. Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. Biochemical Journal. 2012 Mar 15;442(3):527-38.</ref>

PWWP domains are one of the epigenetic regulators which recognize specific lysine residues that are methylated. Even though there is no detailed research on 3pfs, it may be assumed to have similar function with BRPF1 PWWP domain which is shown to have methylated histone binding activity.<ref>Vezzoli A, Bonadies N, Allen MD, Freund SM, Santiveri CM, Kvinlaug BT, Huntly BJ, Göttgens B, Bycroft M. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nature structural & molecular biology. 2010 May;17(5):617-9.</ref> With a high-throughput mass spectrometry screening, 3PFS is also suggested as an essential domain of histone 3 lysine 36 trimethylation binding.<ref>Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010 Sep 17;142(6):967-80.</ref> The β-strands and Pro-Trp-Trp-Pro motif form hydrophobic cavity, which is the binding site of methylated lysines.<ref>Rona GB, Eleutherio EC, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophysical reviews. 2016 Mar 1;8(1):63-74.</ref> Since the aromatic cage is a common structure in the Royal family, it can be a common tool for methylated lysine binding.<ref>Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J. Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. Biochemical Journal. 2012 Mar 15;442(3):527-38.</ref>

[[Image:PWWP surface.png|thumb|center|512 px| '''Figure 2:''' Surface of 3PFS with PWWP motif(green) is indicated. generated in PyMOL using PDB: ''3PFS'']]

Sandbox Reserved 897: Difference between revisions

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 ===Methyl-lysine reader===
-PWWP domains are one of the epigenetic regulators which recognize specific lysine residues that are methylated. Even though there is no detailed research on 3pfs, it may be assumed to have similar function with BRPF1 PWWP domain which is shown to have methylated histone binding activity.<ref>Vezzoli A, Bonadies N, Allen MD, Freund SM, Santiveri CM, Kvinlaug BT, Huntly BJ, Göttgens B, Bycroft M. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nature structural & molecular biology. 2010 May;17(5):617-9.</ref> With a high-throughput mass spectrometry screening, this motif is suggested as an essential motif of histone 3 lysine 36 trimethylation binding.<ref>Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010 Sep 17;142(6):967-80.</ref> The β-strands and Pro-Trp-Trp-Pro motif form hydrophobic cavity, which is the binding site of methylated lysines.<ref>Rona GB, Eleutherio EC, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophysical reviews. 2016 Mar 1;8(1):63-74.</ref> Since the aromatic cage is a common structure in the Royal family, it can be a common tool for methylated lysine binding.<ref>Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J. Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. Biochemical Journal. 2012 Mar 15;442(3):527-38.</ref>
+PWWP domains are one of the epigenetic regulators which recognize specific lysine residues that are methylated. Even though there is no detailed research on 3pfs, it may be assumed to have similar function with BRPF1 PWWP domain which is shown to have methylated histone binding activity.<ref>Vezzoli A, Bonadies N, Allen MD, Freund SM, Santiveri CM, Kvinlaug BT, Huntly BJ, Göttgens B, Bycroft M. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nature structural & molecular biology. 2010 May;17(5):617-9.</ref> With a high-throughput mass spectrometry screening, 3PFS is also suggested as an essential domain of histone 3 lysine 36 trimethylation binding.<ref>Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010 Sep 17;142(6):967-80.</ref> The β-strands and Pro-Trp-Trp-Pro motif form hydrophobic cavity, which is the binding site of methylated lysines.<ref>Rona GB, Eleutherio EC, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophysical reviews. 2016 Mar 1;8(1):63-74.</ref> Since the aromatic cage is a common structure in the Royal family, it can be a common tool for methylated lysine binding.<ref>Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J. Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. Biochemical Journal. 2012 Mar 15;442(3):527-38.</ref>
 [[Image:PWWP surface.png|thumb|center|512 px| '''Figure 2:''' Surface of 3PFS with PWWP motif(green) is indicated. generated in PyMOL using PDB: ''3PFS'']]