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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be an essential part of interaction on H3K36me3.<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 PWWP motif, a part of BRPF proteins, belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of specific methylated histone tail lysine and epigenetic regulation of genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> 3PFS has a β-barrel composed of 5 β-strands, which is a very conservative feature of PWWP domains. The helixes at the C-terminal region are not very conservative; 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is a little different from its name, just like its closely-related proteins. The PWWP domains in the BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of the PWWP motif is that the first position of arrangement affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
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 aromatic residues on 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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives the ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to the PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein varies on species; a man has 20 PWWP containing proteins. The loyal family has a common structural characteristic, three conserved β-strands.<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> Therefore, PWWP domains are believed to be evolved from a common ancestor which had 3 β-strands. Using the domain-tree approach, it is suggested that the BRPF family has branched out from rest of PWWP domain-containing proteins early and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not with the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with Hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene which is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has a very similar structure with its family members. However, further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199501Sandbox Reserved 8972020-04-28T20:29:01Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be an essential part of interaction on H3K36me3.<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 PWWP motif, a part of BRPF proteins, belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of specific methylated histone tail lysine and epigenetic regulation of genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> 3PFS has a β-barrel composed of 5 β-strands, which is a very conservative feature of PWWP domains. The helixes at the C-terminal region are not very conservative; 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is a little different from its name, just like its closely-related proteins. The PWWP domains in the BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of the PWWP motif is that the first position of arrangement affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
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 aromatic residues on 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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives the ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to the PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein varies on species; a man has 20 PWWP containing proteins. The loyal family has a common structural characteristic, three conserved β-strands.<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> Therefore, PWWP domains are believed to be evolved from a common ancestor which had 3 β-strands. Using the domain-tree approach, the BRPF family has branched out from rest of PWWP domain-containing proteins early and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not with the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with Hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene which is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has a very similar structure with its family members. However, further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199500Sandbox Reserved 8972020-04-28T20:26:50Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be an essential part of interaction on H3K36me3.<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 PWWP motif, a part of BRPF proteins, belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of specific methylated histone tail lysine and epigenetic regulation of genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> 3PFS has a β-barrel composed of 5 β-strands, which is a very conservative feature of PWWP domains. The helixes at the C-terminal region are not very conservative; 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is a little different from its name, just like its closely-related proteins. The PWWP domains in the BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of the PWWP motif is that the first position of arrangement affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives the ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to the PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein varies on species; a man has 20 PWWP containing proteins. The loyal family has a common structural characteristic, three conserved β-strands.<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> Therefore, PWWP domains are believed to be evolved from a common ancestor which had 3 β-strands. Using the domain-tree approach, the BRPF family has branched out from rest of PWWP domain-containing proteins early and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not with the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with Hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene which is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has a very similar structure with its family members. However, further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199497Sandbox Reserved 8972020-04-28T20:23:34Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be an essential part of interaction on H3K36me3.<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 PWWP motif, a part of BRPF proteins, belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of specific methylated histone tail lysine and epigenetic regulation of genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> 3PFS has a β-barrel composed of 5 β-strands, which is a very conservative feature of PWWP domains. The helixes at the C-terminal region are not very conservative; 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is a little different from its name, just like its closely-related proteins. The PWWP domains in the BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of the PWWP motif is that the first position of arrangement affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives the ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to the PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein varies on species; a man has 20 PWWP containing proteins. The loyal family has a common structural characteristic, three conserved β-strands.<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> Therefore, PWWP domains are believed to be evolved from a common ancestor which had 3 β-strands. Using the domain-tree approach, the BRPF family has branched out from rest of PWWP domain-containing proteins early and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not with the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with Hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene which is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has a very similar structure with its family members. However, further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199495Sandbox Reserved 8972020-04-28T20:20:15Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be an essential part of interaction on H3K36me3.<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 PWWP motif, a part of BRPF proteins, belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of specific methylated histone tail lysine and epigenetic regulation of genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> 3PFS has a β-barrel composed of 5 β-strands, which is a very conservative feature of PWWP domains. The helixes at the C-terminal region are not very conservative; 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is a little different from its name, just like its closely-related proteins. The PWWP domains in the BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of the PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives the ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to the PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein varies on species; a man has 20 PWWP containing proteins. The loyal family has a common structural characteristic, three conserved β-strands.<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> Therefore, PWWP domains are believed to be evolved from a common ancestor which had 3 β-strands. Using the domain-tree approach, the BRPF family has branched out from rest of PWWP domain-containing proteins early and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not with the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with Hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene which is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has a very similar structure with its family members. However, further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199488Sandbox Reserved 8972020-04-28T20:09:40Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be an essential part of interaction on H3K36me3.<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 PWWP motif, a part of BRPF proteins, belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and epigenetic regulation of genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> 3PFS has a β-barrel composed of 5 β-strands, which is a very conservative feature of PWWP domains. The helixes at the C-terminal region are not very conservative; 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is a little different from its name, just like its closely-related proteins. The PWWP domains in the BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of the PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives the ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to the PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein varies on species; a man has 20 PWWP containing proteins. The loyal family has a common structural characteristic, three conserved β-strands.<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> Therefore, PWWP domains are believed to be evolved from a common ancestor which had 3 β-strands. Using the domain-tree approach, the BRPF family has branched out from rest of PWWP domain-containing proteins early and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not with the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with Hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene which is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has a very similar structure with its family members. However, further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199476Sandbox Reserved 8972020-04-28T19:48:00Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be a essential part of interaction on H3K36me3.<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> Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
[[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'']]<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 3:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. Using domain-tree approach, the BRPF family was branched out from rest of PWWP domain containg proteins and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene wich is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has very similar β-barrel structure with its family members. However, a further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=File:PWWP_surface.png&diff=3199475File:PWWP surface.png2020-04-28T19:46:34Z<p>Sunsik Chang: </p>
<hr />
<div>== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199468Sandbox Reserved 8972020-04-28T19:27:31Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be a essential part of interaction on H3K36me3.<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> Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF1 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. Using domain-tree approach, the BRPF family was branched out from rest of PWWP domain containg proteins and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene wich is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has very similar β-barrel structure with its family members. However, a further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199465Sandbox Reserved 8972020-04-28T19:21:38Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be a essential part of interaction on H3K36me3.<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> Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs alignment.png|thumb|center|512 px| '''Figure 1B:''' The alignment of BRPF2 PWWP domain and BRPF3 PWWP domain. The green box indicates the 'PWWP' motif. generated in Tcoffee using PDB: ''3PFS', '2X35'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. Using domain-tree approach, the BRPF family was branched out from rest of PWWP domain containg proteins and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene wich is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has very similar β-barrel structure with its family members. However, a further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=File:3pfs_alignment.png&diff=3199462File:3pfs alignment.png2020-04-28T19:19:39Z<p>Sunsik Chang: </p>
<hr />
<div>== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199444Sandbox Reserved 8972020-04-28T19:01:23Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be a essential part of interaction on H3K36me3.<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> Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. Using domain-tree approach, the BRPF family was branched out from rest of PWWP domain containg proteins and evolved itself.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref> As a domain, the PWWP presents in both unicellular and multicellular organisms. However, proteins of unicellular organisms are not found in multicellular creatures. Therefore, the PWWP domain was transmitted as a conserved linear arrangement alone, not the whole protein.<ref>Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC evolutionary biology. 2012 Dec 1;12(1):101.</ref><br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene wich is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has very similar β-barrel structure with its family members. However, a further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199441Sandbox Reserved 8972020-04-28T18:50:02Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be a essential part of interaction on H3K36me3.<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> Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene wich is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> The BRPF3 PWWP domain may also have Hox gene-related function since it has very similar β-barrel structure with its family members. However, a further research would be required for more understandings. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199439Sandbox Reserved 8972020-04-28T18:48:12Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and believed to be a essential part of interaction on H3K36me3.<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> Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. <br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between the BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation. BRPF1 PWWP domain presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> BRPF2 is also related to Hox gene wich is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for leukemia, schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref><ref>Laue K, Daujat S, Crump JG, Plaster N, Roehl HH, Kimmel CB, Schneider R, Hammerschmidt M. The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development. 2008 Jun 1;135(11):1935-46.</ref> Therefore BRPF3 PWWP domain, which has very similar β-barrel structure with previous proteins, may also have Hox gene-related function. But a further research would be required. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199437Sandbox Reserved 8972020-04-28T18:43:03Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Bromodomain and PHD finger-containing protein family is the group of proteins found in higher eukaryotes. The members have similar structural features and affinity to genes. Unlike BRPF1 and 2, BRPF3 is less studied by the researchers. Therefore many of its function remains unknown. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation, that is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for leukemia, schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref><ref>Laue K, Daujat S, Crump JG, Plaster N, Roehl HH, Kimmel CB, Schneider R, Hammerschmidt M. The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development. 2008 Jun 1;135(11):1935-46.</ref> Therefore BRPF3 PWWP domain, which has very similar β-barrel structure with previous proteins, may also have Hox gene-related function. But a further research would be required. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199435Sandbox Reserved 8972020-04-28T18:37:47Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation, that is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for leukemia, schizophrenia, and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref><ref>Laue K, Daujat S, Crump JG, Plaster N, Roehl HH, Kimmel CB, Schneider R, Hammerschmidt M. The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development. 2008 Jun 1;135(11):1935-46.</ref> Therefore BRPF3 PWWP domain, which has very similar β-barrel structure with previous proteins, may also have Hox gene-related function. But a further research would be required. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199433Sandbox Reserved 8972020-04-28T18:35:02Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation, that is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref><ref>Laue K, Daujat S, Crump JG, Plaster N, Roehl HH, Kimmel CB, Schneider R, Hammerschmidt M. The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development. 2008 Jun 1;135(11):1935-46.</ref> Therefore BRPF3 PWWP domain, which has very similar β-barrel structure with previous proteins, may also have Hox gene-related function. But a further research would be required. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199432Sandbox Reserved 8972020-04-28T18:30:26Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which 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> <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues which gives ability of nonspecific binding on DNA strands.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> BRPF3 3pfs protein has 11 lysine residues and 12 arginine residues. These residues' sidechains remain being positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, would be attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, both of its closely related domains BRPF1 and BRPF2 PWWP domains are associated with hox gene regulation, that is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> Therefore BRPF3 PWWP domain, which has very similar β-barrel structure with previous proteins, may also have Hox gene-related function. But a further research would be required. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199428Sandbox Reserved 8972020-04-28T18:19:59Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Structure ==<br />
The main characteristic of PWWP domains is the two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and the one at 3pfs is composed of 5 β-strands. The helixes at the C-terminal region are very different and 3pfs has 3 helixes which are little more than many of its relatives. The Pro-Trp-Trp-Pro motif, which is the most conservative, is little different in 3pfs, just like its closely-related proteins. The PWWP domains in BRPF family are composed of Tyr-Pro-Ser-Tyr and may suggest they would have a similar affinity. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. One unique feature of PWWP motif is that the first position affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199424Sandbox Reserved 8972020-04-28T18:11:19Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
<br />
== Function ==<br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 2:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199423Sandbox Reserved 8972020-04-28T18:10:14Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:3pfs cartoon.png|thumb|center|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs non-selective model.png|thumb|center|512 px| '''Figure 1B:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199422Sandbox Reserved 8972020-04-28T18:09:40Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:3pfs cartoon.png|right|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs non-selective model.png|right|512 px| '''Figure 1B:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199421Sandbox Reserved 8972020-04-28T18:08:50Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:3pfs cartoon.png|thumb|right|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:3pfs non-selective model.png|thumb|right|512 px| '''Figure 1B:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface interacting with DNA backbone generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=File:3pfs_non-selective_model.png&diff=3199420File:3pfs non-selective model.png2020-04-28T18:08:12Z<p>Sunsik Chang: 3pfs non-selective model</p>
<hr />
<div>== Summary ==<br />
3pfs non-selective model<br />
== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199390Sandbox Reserved 8972020-04-28T16:29:08Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. The PWWP domain was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein research. The researchers named after its very conservative sequence, Pro-Trp-Trp-Pro located at the β2 strand of protein.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. BRPF1 PWWP domain, which has very similar structure with 3pfs, presents on actively transcribing cells and may regulate Hox A9 gene which is related to MOZ-TIF2-dependant leukemia.<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> The 3pfs motif is relatively mystery we may assume that 3pfs also do similar works<br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:3pfs cartoon.png|thumb|right|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:LYS+ARG.png|thumb|right|512 px| '''Figure 1B:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199385Sandbox Reserved 8972020-04-28T16:15:36Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Its similar protein, BRPF1 PWWP domain presents on actively transcribing cells and we may assume that 3pfs also do similar works.<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> <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:3pfs cartoon.png|thumb|right|512 px| '''Figure 1A:''' Cartoon model of 3PFS motif. β-sheets(magenta) and helixes(orange) are shown. generated in PyMOL using PDB: ''3PFS'']]<br />
[[Image:LYS+ARG.png|thumb|right|512 px| '''Figure 1B:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=File:3pfs_cartoon.png&diff=3199384File:3pfs cartoon.png2020-04-28T16:14:07Z<p>Sunsik Chang: uploaded a new version of "Image:3pfs cartoon.png"</p>
<hr />
<div>== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=File:3pfs_cartoon.png&diff=3199383File:3pfs cartoon.png2020-04-28T16:14:06Z<p>Sunsik Chang: </p>
<hr />
<div>== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199382Sandbox Reserved 8972020-04-28T16:11:49Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Its similar protein, BRPF1 PWWP domain presents on actively transcribing cells and we may assume that 3pfs also do similar works.<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> <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:LYS+ARG.png|thumb|right|512 px| '''Figure 1:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199380Sandbox Reserved 8972020-04-28T16:10:56Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Its similar protein, BRPF1 PWWP domain presents on actively transcribing cells and we may assume that 3pfs also do similar works.<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> <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:LYS+ARG.png|thumb|left|512 px|alt=Figure 1B: Emixustat and palmitate ester in Binding Pocket| '''Figure 1:''' Lysine(yellow) and Arginine(red) residues on 3PFS surface generated in PyMOL using PDB: ''3PFS'']]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=File:LYS%2BARG.png&diff=3199378File:LYS+ARG.png2020-04-28T16:07:39Z<p>Sunsik Chang: uploaded a new version of "Image:LYS+ARG.png"</p>
<hr />
<div>== Summary ==<br />
3pfs lys+arg<br />
== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199377Sandbox Reserved 8972020-04-28T16:05:46Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Its similar protein, BRPF1 PWWP domain presents on actively transcribing cells and we may assume that 3pfs also do similar works.<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> <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:LYS+ARG.png]]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=File:LYS%2BARG.png&diff=3199376File:LYS+ARG.png2020-04-28T16:05:17Z<p>Sunsik Chang: 3pfs lys+arg</p>
<hr />
<div>== Summary ==<br />
3pfs lys+arg<br />
== Licensing ==<br />
{{PD-self}}</div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199375Sandbox Reserved 8972020-04-28T16:03:46Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Its similar protein, BRPF1 PWWP domain presents on actively transcribing cells and we may assume that 3pfs also do similar works.<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> <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges.<br />
[[Image:Example.jpg]]<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199315Sandbox Reserved 8972020-04-28T04:59:32Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. Its similar protein, BRPF1 PWWP domain presents on actively transcribing cells and we may assume that 3pfs also do similar works.<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> <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges. 사진1<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
There is no research on the relationship between BRPF3 PWWP domain and any human disease. However, its sibling gene BRPF2 PWWP domain is associated with schizophrenia and bipolar affective disorder.<ref>Bjarkam CR, Corydon TJ, Olsen IM, Pallesen J, Nyegaard M, Fryland T, Mors O, Børglum AD. Further immunohistochemical characterization of BRD1 a new susceptibility gene for schizophrenia and bipolar affective disorder. Brain Structure and Function. 2009 Dec 1;214(1):37.</ref> <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199310Sandbox Reserved 8972020-04-28T04:06:43Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
===Nonspecific binding===<br />
The PWWP domains have a significant amount of basic residues.<ref>Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature structural biology. 2002 Mar;9(3):217-24.</ref> 3pfs also has 11 lysine residues and 12 arginine residues. These residues' sidechains would be positively charged on in vivo pH. The DNA strand phosphate backbone, which is negatively charged, is attracted to PWWP domain surface due to the nature of attraction between the opposite charges. 사진1<br />
<br />
===Methyl-lysine reader===<br />
PWWP domains are one of epigenetic regulators which recognize specific lysine residues which are methylated. Even though there is no detailed research on 3pfs, it is 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> <br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is a very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. <br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199305Sandbox Reserved 8972020-04-28T03:11:58Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
<br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref> It has two distinctive substructural motifs: β-barrel at the N-terminal region and helixes at C-terminal region.<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> The β-barrel is very conservative feature of PWWP domains and it is composed of 5 β-strands. 3pfs has 3 helixes which are little more than many of its relatives. The stability of domain comes from both inter-substructure and intra-substructure interactions including hydrogen bonds and polar interactions. 11K 12R<br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
<br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref><br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The PWWP domain is also believed to be evolved from a common ancestor which had 3 β-strands. The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
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<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids in WHSC1 protein. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
<br />
<br />
== Structure ==<br />
Two disticntive The first proline affects the stability and aggregation of the protein. The proline gives more stability and oligomerization to the protein, compared to the alanine at the same position.<ref>Hung YL, Lee HJ, Jiang I, Lin SC, Lo WC, Lin YJ, Sue SC. The first residue of the PWWP motif modulates HATH domain binding, Stability, and Protein–Protein Interaction. Biochemistry. 2015 Jul 7;54(26):4063-74.</ref><br />
<br />
=== Evolutionary conservations ===<br />
PWWP domain is only found in eukaryotes, from a yeast to a human. The number of PWWP containing protein is also varying on species; the human has 20. The loyal family has a common structural characteristic, three conserved β-strands.<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> The most conservative section is the PWWP sequence, which it is named after. <br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3199135Sandbox Reserved 8972020-04-26T22:33:39Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related to the recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
== Structure ==<br />
The first proline affects the stability and aggregation of the protein.<br />
<br />
=== Evolutionary conservations ===<br />
The loyal family has a common structural characteristic, three conserved β-strands.<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> <br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198985Sandbox Reserved 8972020-04-26T04:12:14Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> This domain is mainly related with recognition of methylated histone tail lysine and related to the epigenetic regulation of genes. <br />
<br />
== Function ==<br />
The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
== Structure ==<br />
The first proline affects the stability and aggregation of the protein.<br />
<br />
=== Evolutionary conservations ===<br />
<br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198732Sandbox Reserved 8972020-04-23T18:00:41Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> The first proline affects the stability and aggregation of the protein. The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
== Function ==<br />
<br />
== Structure ==<br />
<br />
=== Evolutionary conservations ===<br />
<br />
== Therapheutic features ==<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198731Sandbox Reserved 8972020-04-23T17:58:37Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> The first proline affects the stability and aggregation of the protein. The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with a DNA strand, using its abundant lysine and arginine residues. <br />
<br />
== Function ==<br />
<br />
== Structure ==<br />
<br />
=== Evolution ===<br />
<br />
== Therapheutic features ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198658Sandbox Reserved 8972020-04-22T23:42:19Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> The first proline affects the stability and aggregation of the protein. The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with DNA strand, using its abundant lysin and arginine residues. <br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198654Sandbox Reserved 8972020-04-22T23:37:07Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> The first proline affects the stability and aggregation of the protein. The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with DNA strand, using its abundant lysin and arginine residues. <br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
=structure=<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198653Sandbox Reserved 8972020-04-22T23:35:20Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT(Malignant Brain Tumor), and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<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> The first proline affects the stability and aggregation of the protein. The PWWP domain is also used for protein-protein interaction. This domain also may have nonspecific interaction with DNA strand, using its abundant lysin and arginine residues. <br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198649Sandbox Reserved 8972020-04-22T23:19:35Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT, and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region.<ref>Chen T, Tsujimoto N, Li E. The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. Molecular and cellular biology. 2004 Oct 15;24(20):9048-58.</ref> <br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198648Sandbox Reserved 8972020-04-22T23:17:29Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
The PWWP domain belongs to the Royal family, which consists of Tudor, chromodomain, MBT, and PWWP domains. It was first identified as a structural motif includes 100 to 130 amino acids. The name PWWP comes after its very conservative sequence, Pro-Trp-Trp-Pro located at its β2 region. <ref>Chen T, Tsujimoto N, Li E. The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. Molecular and cellular biology. 2004 Oct 15;24(20):9048-58.</ref> <br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198647Sandbox Reserved 8972020-04-22T23:02:34Z<p>Sunsik Chang: </p>
<hr />
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==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
Hi<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Changhttps://proteopedia.org/index.php?title=Sandbox_Reserved_897&diff=3198646Sandbox Reserved 8972020-04-22T23:02:00Z<p>Sunsik Chang: </p>
<hr />
<div>{{Sandbox_reserved_Karen_Glass_2020}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==BRPF3 PWWP binding domain 3PFS==<br />
<StructureSection load='3pfs' size='340' side='right' caption='BRPF3 PWWP domain' scene=''><br />
<br />
== Overview ==<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Sunsik Chang