https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Samuel+Carlson 2026-10-04T13:38:40Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792922 2013-05-07T20:10:10Z

<p>Samuel Carlson: /* Medical Implications */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a transcription factor which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> The PHD finger domain of BAZ2a may also bind histones, as its structure and sequence are similar to those of other PHD fingers, which have been shown to bind to methylated lysine residues on H3. &lt;ref&gt;PMID:17142463&lt;/ref&gt;&lt;ref&gt;PMID:1672897&lt;/ref&gt;<br /> <br /> The PHD finger and Bromodomain may act together to recognize posttranslationally modified histones, as is the case in the human Bromodomain PHD transcription factor BPTF.&lt;ref&gt;PMID:21596426&lt;/ref&gt;<br /> <br /> <br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, the bromodomain of BAZ2a and other bromodomains with more evolutionarily similar sequences have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792920 2013-05-07T20:08:27Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a transcription factor which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> The PHD finger domain of BAZ2a may also bind histones, as its structure and sequence are similar to those of other PHD fingers, which have been shown to bind to methylated lysine residues on H3. &lt;ref&gt;PMID:17142463&lt;/ref&gt;&lt;ref&gt;PMID:1672897&lt;/ref&gt;<br /> <br /> The PHD finger and Bromodomain may act together to recognize posttranslationally modified histones, as is the case in the human Bromodomain PHD transcription factor BPTF.&lt;ref&gt;PMID:21596426&lt;/ref&gt;<br /> <br /> <br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792919 2013-05-07T20:07:37Z

<p>Samuel Carlson: /* Histone Recognition */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a transcription factor which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> The PHD finger domain of BAZ2a may also bind histones, as its structure and sequence are similar to those of other PHD fingers, which have been shown to bind to methylated lysine residues on H3. &lt;ref&gt;PMID:17142463&lt;/ref&gt;&lt;ref&gt;PMID:1672897&lt;/ref&gt;<br /> <br /> The PHD finger and Bromodomain may act together to recognize posttranslationally modified histones, as is the case in the human Bromodomain PHD transcription factor BPTF.&lt;ref&gt;PMID:21596426&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792916 2013-05-07T20:06:14Z

<p>Samuel Carlson: /* Overview */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a transcription factor which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> The PHD finger domain may also bind histones, as its structure and sequence are similar to those of other PHD fingers, which have been shown to bind to methylated lysine residues on H3. &lt;ref&gt;PMID:17142463&lt;/ref&gt;&lt;ref&gt;PMID:1672897&lt;/ref&gt;<br /> <br /> The PHD finger and Bromodomain may act together to recognize posttranslationally modified histones, as is the case in the human Bromodomain PHD transcription factor BPTF.&lt;ref&gt;PMID:21596426&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792914 2013-05-07T20:05:10Z

<p>Samuel Carlson: /* Histone Recognition */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> The PHD finger domain may also bind histones, as its structure and sequence are similar to those of other PHD fingers, which have been shown to bind to methylated lysine residues on H3. &lt;ref&gt;PMID:17142463&lt;/ref&gt;&lt;ref&gt;PMID:1672897&lt;/ref&gt;<br /> <br /> The PHD finger and Bromodomain may act together to recognize posttranslationally modified histones, as is the case in the human Bromodomain PHD transcription factor BPTF.&lt;ref&gt;PMID:21596426&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792909 2013-05-07T20:03:18Z

<p>Samuel Carlson: /* Histone Recognition */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> The PHD finger domain may also bind histones, as its structure and sequence are similar to those of other PHD fingers, which have been shown to bind to methylated lysine residues on H3. &lt;ref&gt;PMID:17142463&lt;/ref&gt;&lt;ref&gt;PMID:1672897&lt;/ref&gt;<br /> <br /> The PHD finger and Bromodomain may act together to recognize posttranslationally modified histones, as is the case in BPTF.&lt;ref&gt;PMID:21596426&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792884 2013-05-07T19:40:48Z

<p>Samuel Carlson: /* Evolution and related structures */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures can be found at pages linked below, for PHD finger and Bromodomain categories on Proteopedia. [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792883 2013-05-07T19:39:12Z

<p>Samuel Carlson: /* Overview */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor (DDT) domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus.<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures: [[Category:Phd_finger]]; [[Category:Bromodomain]]; [[3g0l]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792881 2013-05-07T19:38:18Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[3g0l]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures: [[Category:Phd_finger]]; [[Category:Bromodomain]]; [[3g0l]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]][[Image:Bromodomain_With_Ligand.png|thumb|200px|left|BRPF1, showing interaction of secondary structure with ligand H4K5ac]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792875 2013-05-07T19:29:11Z

<p>Samuel Carlson: /* Histone Recognition */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures: [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromodomain_With_Ligand.png|thumb|300px|BRPF1, showing interaction of secondary structure with ligand H4K5ac]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=File:Bromodomain_With_Ligand.png&diff=1792874 2013-05-07T19:26:31Z

<p>Samuel Carlson: BRPF1 Bromodomain with ligand H4K5ac.</p> <hr /> <div>BRPF1 Bromodomain with ligand H4K5ac.</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792872 2013-05-07T19:24:31Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> Additional domain structures: [[Category:Phd_finger]]; [[Category:Bromodomain]]<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]][[Image:Bromo Binding Site.png|thumb|300px|Binding site of BAZ2b, showing conserved hydrophobic residues (yellow) and absolutely conserved Asn involved in hydrogen bonding]] The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=File:Bromo_Binding_Site.png&diff=1792860 2013-05-07T18:58:27Z

<p>Samuel Carlson: Map of BAZ2b binding site showing hydrophobic residues in yellow and hydrogen bonding residues in red.</p> <hr /> <div>Map of BAZ2b binding site showing hydrophobic residues in yellow and hydrogen bonding residues in red.</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792768 2013-05-07T17:18:21Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt; The structures of individual domains (PHD fingers, Bromodomains, MBD domains, and DDT domains) similar to those found in BAZ2a have been solved.<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]]The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription. &lt;ref&gt;PMID:19680546&lt;/ref&gt; Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792706 2013-05-07T16:28:31Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> [[Image:Bromodomain Alignment.jpg|thumb|400px|left|BAZ2a and other bromodomain sequences aligned to show conserved Kac binding residues.]]The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792698 2013-05-07T16:22:57Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> [[Image:Bromodomain Alignment.jpg]]<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=File:Bromodomain_Alignment.jpg&diff=1792697 2013-05-07T16:21:58Z

<p>Samuel Carlson: Bromodomain sequences aligned to show conserved residues in acetyllysine binding pocket.</p> <hr /> <div>Bromodomain sequences aligned to show conserved residues in acetyllysine binding pocket.</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792535 2013-05-07T08:08:47Z

<p>Samuel Carlson: /* Histone Recognition */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> The highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792534 2013-05-07T08:07:50Z

<p>Samuel Carlson: /* Histone Recognition */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> he highly-conserved bromodomain of BAZ2a is likely to bind acetylated lysine residues of histones, particularly the tails. Bromodomains have a high degree of specificity for acetylation marks, due to several key residues in the binding pocket, which is composed of the ends of the four alpha helices and the ZA-loop. The binding pocket is composed primarily of hydrophobic residues such as Val, Tyr, and Phe, which interact hydrophobically with the histone tail. &lt;ref&gt;pmid:10365964&lt;/ref&gt; Specificity for acetylated histones in other bromodomains is likely caused by hydrogen bonding with the Asn residue in the binding pocket. &lt;ref&gt;pmid:10365964&lt;/ref&gt;<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792499 2013-05-07T07:16:49Z

<p>Samuel Carlson: /* Medical Implications */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomain families have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding pockets, due to certain amino acid signatures. &lt;ref&gt;PMID:22788793&lt;/ref&gt; However, BAZ2a and other proteins with bromodomains that contain similar sequences in their binding pockets have not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792498 2013-05-07T07:13:16Z

<p>Samuel Carlson: /* Medical Implications */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomains have been identified as potent drug targets for inhibitors&lt;ref&gt;PMID:20871596&lt;/ref&gt;, specifically at their acetyl-lysine binding sites&lt;ref&gt;PMID:22788793&lt;/ref&gt;. However, BAZ2a has not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792492 2013-05-07T07:08:20Z

<p>Samuel Carlson: /* Medical Implications */</p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt; Other bromodomains have been identified as potent drug targets for inhibitors &lt;ref&gt;PMID:22788793&lt;/ref&gt; &lt;ref&gt;PMID:20871596&lt;/ref&gt; but BAZ2a has not been investigated yet.<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792458 2013-05-07T06:21:34Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> ==Overview==<br /> {{align|right|'''Bromodomain of BAZ2b, similar to BAZ2a'''}}<br /> {{STRUCTURE_3g0l| PDB=3g0l | SIZE=400| SCENE= |right|CAPTION=Human BAZ2b bromodomain structure, BAZ2a bromodomain is assumed similar [[1rgw]] }}<br /> BAZ2A is a chromatin remodeling protein which acts as a regulator of chromatin remodeling. It is part of the nucleolar remodeling complex (NoRC).<br /> This structure consists of a methyl-CpG binding domain (MBD) near the N-terminus, a DNA-binding homeobox and different transcription factor domain, and a plant homeodomain (PHD) zinc finger next to a bromodomain on the N-terminus. <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:NoRC_complex_diagram.png|thumb|166px|left|BAZ2A and SNF2H make up the Nucleolar Remodeling Complex.]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases&lt;ref&gt;PMID:16678107&lt;/ref&gt;, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues.&lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> ==Histone Recognition==<br /> <br /> ==DNA and RNA binding==<br /> Because of a methyl-CPG binding domain and two AT hooks, BAZ2a binds to DNA with high affinity, with no specificity for methylation.&lt;ref&gt;PMID:11532953&lt;/ref&gt;<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> Recent studies have shown that BAZ2a depletion causes suppression of chromatin remodeling and increases rRNA transcription (CITE). Loss of BAZ2a functionality can therefore lead to genetic instability, phenotypic transformation, and cell proliferation beyond confluence. &lt;ref&gt;PMID:20168299&lt;/ref&gt;<br /> <br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=File:NoRC_complex_diagram.png&diff=1792375 2013-05-07T05:04:43Z

<p>Samuel Carlson: The Nucleolar Remodeling Complex, composed of BAZ2A and SNF2H, recruits other proteins to remodel chromatin and silence transcription.</p> <hr /> <div>The Nucleolar Remodeling Complex, composed of BAZ2A and SNF2H, recruits other proteins to remodel chromatin and silence transcription.</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792370 2013-05-07T05:01:25Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> <br /> {{STRUCTURE_3g0l| PDB=3g0l | SCENE= }} <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> [[Image:Example.jpg]]<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. (CITE) BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues. <br /> <br /> ==Evolution and related structures==<br /> The bromodomain is a highly conserved structure within BAZ2a. It can be found in many large proteins associated with helicase activity, chromatin remodeling, methyl- or acetyltransferase activity, or transcriptional control. &lt;ref&gt;PMID:22464331&lt;/ref&gt;<br /> <br /> =BAZ2a Function=<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792279 2013-05-07T03:57:33Z

<p>Samuel Carlson: </p> <hr /> <div>=Bromodomain adjacent to zinc finger domain protein 2A (BAZ2a)=<br /> &lt;StructureSection load='3g0l' size='350' side='right' caption='Structure of BAZ2b bromodomain (PDB entry [[3g0l]]), BAZ2a similar' scene=''&gt;<br /> Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br /> <br /> &lt;/StructureSection&gt;<br /> <br /> {{STRUCTURE_3g0l| PDB=3g0l | SCENE= }} <br /> <br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. (CITE) BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues. <br /> <br /> ==Evolution and related structures==<br /> The bromodomain of BAZ2a is highly conserved across <br /> <br /> =BAZ2a Function=<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792234 2013-05-07T03:33:35Z

<p>Samuel Carlson: </p> <hr /> <div>== Bromodomain Structure ==<br /> &lt;StructureSection load='3g0l' size='350' side='right' caption='Structure of BAZ2b bromodomain (PDB entry [[3g0l]]), BAZ2a similar' scene=''&gt;<br /> Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br /> <br /> &lt;/StructureSection&gt;<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. (CITE) BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues. <br /> <br /> = BAZ2a Function=<br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==<br /> <br /> =References=<br /> &lt;references/&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792221 2013-05-07T03:27:16Z

<p>Samuel Carlson: </p> <hr /> <div>== Bromodomain Structure ==<br /> &lt;StructureSection load='3g0l' size='350' side='right' caption='Structure of BAZ2b bromodomain (PDB entry [[3g0l]]), BAZ2a similar' scene=''&gt;<br /> Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br /> <br /> &lt;/StructureSection&gt;<br /> <br /> ==Role in the Nucleolar Remodeling Complex (NoRC)==<br /> BAZ2A interacts with sucrose-nonfermenting protein 2 homolog (SNF2H) to form the NoRC, which recruits histone methyltransferases, histone deacetylases, and DNA methyltransferases. The NoRC silences transcription by modifying DNA compaction, as well as by interfering with ribosomal RNA (rRNA) transcription. (CITE) BAZ2a is thought to direct transcriptional repression by binding to histones labeled with posttranslational modifications (PTMs) such as acetylation on lysine residues. <br /> <br /> <br /> ==Role in Chromatin Remodeling==<br /> As a critical member of the NoRC, BAZ2a in conjunction with SNF2H is responsible for modifying the compaction of chromatin, through <br /> The NoRC is also responsible for ribosomal DNA (rDNA) transcription silencing, by recruiting histone deacetylase (HDAC) and DNA methyltransferase (DNMT) to the rDNA promoter, effectively creating a region with the characteristics of heterochromatin and silencing rDNA transcription. &lt;ref&gt;PMID:12368916&lt;/ref&gt;<br /> <br /> ==Medical Implications==</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson/Sandbox_1&diff=1792180 2013-05-07T03:00:03Z

<p>Samuel Carlson: New page: == Bromodomain Structure == &lt;StructureSection load=&#039;3g0l&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Structure of BAZ2b bromodomain (PDB entry 3g0l), BAZ2a similar&#039; scene=&#039;&#039;&gt; Anything in this se...</p> <hr /> <div>== Bromodomain Structure ==<br /> &lt;StructureSection load='3g0l' size='350' side='right' caption='Structure of BAZ2b bromodomain (PDB entry [[3g0l]]), BAZ2a similar' scene=''&gt;<br /> Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br /> <br /> &lt;/StructureSection&gt;</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson&diff=1792173 2013-05-07T02:53:33Z

<p>Samuel Carlson: </p> <hr /> <div>* Full Real Name: Samuel Carlson<br /> <br /> * Position: Research Assistant<br /> <br /> * Institution (NO ABBREVIATIONS): Albany College of Pharmacy and Health Sciences<br /> <br /> * City, State/Province, Country: Colchester, Vermont, USA<br /> <br /> * Field of Expertise or Study: Molecular Biology. B.A. in Biology at Middlebury College, VT.<br /> <br /> *[[User:Samuel Carlson/Sandbox 1]]</div>

Samuel Carlson https://proteopedia.org/index.php?title=User:Samuel_Carlson&diff=1792169 2013-05-07T02:51:29Z

<p>Samuel Carlson: </p> <hr /> <div>* Full Real Name: Samuel Carlson<br /> <br /> * Position: Research Assistant<br /> <br /> * Institution (NO ABBREVIATIONS): Albany College of Pharmacy and Health Sciences<br /> <br /> * City, State/Province, Country: Colchester, Vermont, USA<br /> <br /> * Field of Expertise or Study: Molecular Biology. B.A. in Biology at Middlebury College, VT.<br /> <br /> User:Samuel Carlson/Sandbox 1</div>

Samuel Carlson