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https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Juliet+Obi Proteopedia - User contributions [en] 2026-09-18T09:19:25Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2840981 User:Juliet Obi/Sandbox 1 2018-01-09T16:29:48Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A (BAZ1A)==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|thumb|alt=BAZ1A anchor and gatekeeper residues|Fig.1:The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B bromodomains|Fig.2:BAZ1A and BAZ1B both have a conserved asparagine anchor (in yellow) but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B (in red), present in the binding pockets of several acetyl-lysine binding bromodomains. Sequence alignment was carried out using Tcoffee <ref name="do:regular">http://tcoffee.crg.cat/apps/tcoffee/do:regular</ref>]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B PHD finger motifs|Fig.3:BAZ1A has a positively charged feature (highlighted in red), absent in BAZ1B suggesting that it potentially binds to a negatively charged feature such as DNA. Sequence alignment was carried out using Tcoffee <ref name="do:regular"/>]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png|thumb|center|alt=Protein-ligand interaction of BAZ1A|Fig.4:BAZ1A has its structure solved with a unique ligand EPE on chains B and D. The image shows a pymol structure of BAZ1A and the EPE ligand in spheres on chains B and D. PDB ID: 5UIY]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=Bromodomain_adjacent_to_zinc_finger&diff=2840980 Bromodomain adjacent to zinc finger 2018-01-09T16:28:50Z

<p>Juliet Obi: New page: ==Bromodomain Adjacent to Zinc Finger domain 1A (BAZ1A)== <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry 5uiy)...</p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A (BAZ1A)==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|thumb|alt=BAZ1A anchor and gatekeeper residues|Fig.1:The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B bromodomains|Fig.2:BAZ1A and BAZ1B both have a conserved asparagine anchor (in yellow) but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B (in red), present in the binding pockets of several acetyl-lysine binding bromodomains. Sequence alignment was carried out using Tcoffee <ref name="do:regular">http://tcoffee.crg.cat/apps/tcoffee/do:regular</ref>]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B PHD finger motifs|Fig.3:BAZ1A has a positively charged feature (highlighted in red), absent in BAZ1B suggesting that it potentially binds to a negatively charged feature such as DNA. Sequence alignment was carried out using Tcoffee <ref name="do:regular"/>]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png|thumb|center|alt=Protein-ligand interaction of BAZ1A|Fig.4:BAZ1A has its structure solved with a unique ligand EPE on chains B and D. The image shows a pymol structure of BAZ1A and the EPE ligand in spheres on chains B and D. PDB ID: 5UIY]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2840979 User:Juliet Obi/Sandbox 1 2018-01-09T15:46:41Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|thumb|alt=BAZ1A anchor and gatekeeper residues|Fig.1:The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B bromodomains|Fig.2:BAZ1A and BAZ1B both have a conserved asparagine anchor (in yellow) but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B (in red), present in the binding pockets of several acetyl-lysine binding bromodomains. Sequence alignment was carried out using Tcoffee <ref name="do:regular">http://tcoffee.crg.cat/apps/tcoffee/do:regular</ref>]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B PHD finger motifs|Fig.3:BAZ1A has a positively charged feature (highlighted in red), absent in BAZ1B suggesting that it potentially binds to a negatively charged feature such as DNA. Sequence alignment was carried out using Tcoffee <ref name="do:regular"/>]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png|thumb|center|alt=Protein-ligand interaction of BAZ1A|Fig.4:BAZ1A has its structure solved with a unique ligand EPE on chains B and D. The image shows a pymol structure of BAZ1A and the EPE ligand in spheres on chains B and D. PDB ID: 5UIY]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2840978 User:Juliet Obi/Sandbox 1 2018-01-09T15:04:18Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|thumb|alt=BAZ1A anchor and gatekeeper residues|Fig.1:The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B bromodomains|Fig.2:BAZ1A and BAZ1B both have a conserved asparagine anchor (in yellow) but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B (in red), present in the binding pockets of several acetyl-lysine binding bromodomains. Sequence alignment was carried out using Tcoffee <ref name="do:regular">http://tcoffee.crg.cat/apps/tcoffee/do:regular</ref>]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B PHD finger motifs|Fig.3:BAZ1A has a positively charged feature (highlighted in red), absent in BAZ1B suggesting that it potentially binds to a negatively charged feature such as DNA. Sequence alignment was carried out using Tcoffee <ref name="do:regular"/>]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2838570 User:Juliet Obi/Sandbox 1 2017-12-27T22:14:04Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|thumb|alt=BAZ1A anchor and gatekeeper residues|Fig.1:The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG|thumb|center|alt=Sequence alignment of BAZ1A and BAZ1B bromodomains|Fig.2:BAZ1A and BAZ1B both have a conserved asparagine anchor (in yellow) but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B (in red), present in the binding pockets of several acetyl-lysine binding bromodomains. Sequence alignment was carried out using Tcoffee <ref>http://tcoffee.crg.cat/apps/tcoffee/do:regular</ref>]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2838569 User:Juliet Obi/Sandbox 1 2017-12-27T21:44:46Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|thumb|alt=BAZ1A anchor and gatekeeper residues|Fig.1:The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2838568 User:Juliet Obi/Sandbox 1 2017-12-27T21:07:47Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png|Fig. 1: BAZ1A anchor and gatekeeper residues. The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues coloured in magenta)]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2838567 User:Juliet Obi/Sandbox 1 2017-12-27T19:03:43Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="humu.23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling <ref name="humu.23034"/>. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2838566 User:Juliet Obi/Sandbox 1 2017-12-27T18:51:55Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A is a monomer and has its structure solved with a unique ligand, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (EPE), on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below (PDBID: 5UIY)<br /> <br /> === BAZ1A protein-ligand interaction ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2836428 User:Juliet Obi/Sandbox 1 2017-12-24T19:53:50Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>PMID:12192034</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2836427 User:Juliet Obi/Sandbox 1 2017-12-24T19:52:34Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>DOI 10.1128/mcb.22.18.6344-6353.2002</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2836426 User:Juliet Obi/Sandbox 1 2017-12-24T19:48:55Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC (Williams Syndrome Transcription Factor WSTF/ ATP-utilizing chromatin assembly and remodeling factor 1 ACF1/ mouse protein related to ACF1 Cbp146) motif found in WSTF/ACF1/cbp146-related proteins <ref>DOI 10.1128/MCB.22.18.6344-6353.2002</ref> and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 (WSTF-, ACF1- like protein 1) <ref>DOI 10.1093/emboj/19.13.3377</ref> <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831540 User:Juliet Obi/Sandbox 1 2017-12-07T18:47:20Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831539 User:Juliet Obi/Sandbox 1 2017-12-07T18:46:01Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref name="23034">DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features and comparison with WAL family member BAZ1B ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Conservation ==<br /> <br /> BAZ1A appears to be conserved 100% among various species apart from humans. Popular organisms with conserved BAZ1A including humans are mice, zebrafish, rats and bovine animals. BAZ1A also has the evolutionarily conserved glutamic acid gatekeeper which reduces its affinity for binding to acetyl-lysine histone ligands. Substitution of the glutamic acid with a canonical valine gatekeeper has been found to increase its binding to acetyl-lysine histone ligands as well as DNA damage hypersensitivity. This suggests the evolution of BAZ1A to bind acetylated histone ligands with a specific affinity and increasing or decreasing this affinity may prevent BAZ1A from functioning in DNA damage recovery <ref name="s41467"/>.<br /> <br /> == Disease implications of BAZ1A ==<br /> <br /> There is limited knowledge on the functions of BAZ1A in disease conditions. Recent studies have shown the role of BAZ1A in neurodevelopment and a potential link of BAZ1A to intellectual disability (ID) by showing data of its role on three pathways including vitamin D regulation, Wnt signalling, and postsynaptic signalling. These findings support the growing evidence for the role of chromatin-remodeling factors in cognition with more studies to be carried out in the future <ref name="23034"/>.<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested. However, studies have shown the importance of BAZ1A in DNA damage recovery, partly by regulating the fucntion of ISWI chromatin remodelers at DNA damage sites and supporting transcriptional activity required for survival <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831538 User:Juliet Obi/Sandbox 1 2017-12-07T17:46:44Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), Williams syndrome transcription factor-related chromatin remodeling factor 180 (WCRF180), hACF1 or WALp1 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831505 User:Juliet Obi/Sandbox 1 2017-12-07T06:08:48Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> [[Image:BAZ1A protein-ligand interaction.png]]<br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=File:BAZ1A_protein-ligand_interaction.png&diff=2831504 File:BAZ1A protein-ligand interaction.png 2017-12-07T06:07:31Z

<p>Juliet Obi: BAZ1A interaction with its unique ligand EPE on chains B and D. The ligand is shown as the orange and blue spheres</p> <hr /> <div>BAZ1A interaction with its unique ligand EPE on chains B and D. The ligand is shown as the orange and blue spheres</div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831503 User:Juliet Obi/Sandbox 1 2017-12-07T06:05:34Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B (1601) and D (1601). A pymol structure showing the ligands in spheres on chains B and D is shown in the image below. <br /> <br /> === BAZ1A protein-ligand interactions ===<br /> <br /> <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831502 User:Juliet Obi/Sandbox 1 2017-12-07T06:01:32Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain (indicated in red in the figure below). The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions (indicated in red in the image below). The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> === Sequence alignment of BAZ1A and BAZ1B PHD fingers ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG]]<br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=File:BAZ1A_and_BAZ1B_PHD_Sequence_Alignment.PNG&diff=2831501 File:BAZ1A and BAZ1B PHD Sequence Alignment.PNG 2017-12-07T05:57:38Z

<p>Juliet Obi: Sequence alignment of BAZ1A and BAZ1B PHD finger motifs using Tcoffee. BAZ1A has a positively charged feature absent in BAZ1B suggesting it potentially binds to a negatively charged feature such as DNA.</p> <hr /> <div>Sequence alignment of BAZ1A and BAZ1B PHD finger motifs using Tcoffee. BAZ1A has a positively charged feature absent in BAZ1B suggesting it potentially binds to a negatively charged feature such as DNA.</div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831500 User:Juliet Obi/Sandbox 1 2017-12-07T05:53:24Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === Sequence alignment of BAZ1A and BAZ1B bromodomains ===<br /> <br /> [[Image:BAZ1A_and_BAZ1B_sequence_alignment.PNG]]<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=File:BAZ1A_and_BAZ1B_sequence_alignment.PNG&diff=2831499 File:BAZ1A and BAZ1B sequence alignment.PNG 2017-12-07T05:47:48Z

<p>Juliet Obi: Sequence alignment of BAZ1A and BAZ1B bromodomains. BAZ1A and BAZ1B both have a conserved asparagine anchor but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B which is present in the binding pockets of several</p> <hr /> <div>Sequence alignment of BAZ1A and BAZ1B bromodomains. BAZ1A and BAZ1B both have a conserved asparagine anchor but BAZ1A has a glutamic acid gatekeeper residue instead of a valine gatekeeper residue in BAZ1B which is present in the binding pockets of several acetyl-lysine binding bromodomains. Sequence alignment was carried out using Tcoffee.</div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831498 User:Juliet Obi/Sandbox 1 2017-12-07T05:42:16Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> ====<br /> <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831497 User:Juliet Obi/Sandbox 1 2017-12-07T05:36:49Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. [[Image:BAZ1A_anchor_gatekeeper_residues.png | thumb]]<br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=File:BAZ1A_anchor_gatekeeper_residues.png&diff=2831496 File:BAZ1A anchor gatekeeper residues.png 2017-12-07T05:34:19Z

<p>Juliet Obi: The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues colored in magenta)</p> <hr /> <div>The bromodomain of BAZ1A has the asparagine anchor residue required for binding and a non-canonical glutamic acid gatekeeper residue (residues colored in magenta)</div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831495 User:Juliet Obi/Sandbox 1 2017-12-07T05:28:32Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A and BAZ1B belong to the WAL family of bromodomains. Both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831494 User:Juliet Obi/Sandbox 1 2017-12-07T05:16:40Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==<br /> <references/></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2831493 User:Juliet Obi/Sandbox 1 2017-12-07T05:15:38Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> <br /> == References ==</div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828521 User:Juliet Obi/Sandbox 1 2017-12-02T06:02:51Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand <scene name='77/774674/Epe/1'>EPE</scene>, on chains B and D. The ligand is surrounded mainly by hydrophobic residues, as well as aromatic and electrically charged residues. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. A decrease in BAZ1A expression impairs recovery from DNA damage in human cells <ref>DOI 10.1016/j.molcel.2010.12.003</ref> <ref>DOI 10.1083/jcb.201405077</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828520 User:Juliet Obi/Sandbox 1 2017-12-02T05:51:24Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand <scene name='77/774674/Epe/1'>EPE</scene>, on chains B and D. The ligand is surrounded mainly by hydrophobic residues, as well as aromatic and electrically charged residues. <br /> <br /> == Medical importance ==<br /> <br /> BAZ1A in complex with SMARCA5 has been implicated in different DNA repair mechanisms <ref>DOI 10.4161/15384101.2014.956551</ref>. Mutations in the PHD of BAZ1A can disrupt DNA binding and cause transcriptional deregulation before or after DNA damage. The specific target(s) of BAZ1A to DNA damage sites remain unknown, although there is an hypothesis that the DNA binding surface of BAZ1A-PHD is required for disengaging BAZ1A from chromatin after a DNA repair process but it needs to be tested <ref name="s41467"/>. <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828518 User:Juliet Obi/Sandbox 1 2017-12-02T05:17:25Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. However, BAZ1A-PHD has been found to contain a positively charged feature possibly due to the closely spaced lysine residues on the K1181 and K1183 positions. The positive charge could be involved in binding a negatively charged partner such as DNA and studies have shown binding affinities tests to confirm this <ref name="s41467"/>. Although the N-terminal WAC motif of BAZ1A has been shown to bind nucleosomes by a linker DNA in the regulation of the BAZ1A-SMARCA5 complex (ACF complex) <ref>DOI 10.1038/nature13380</ref>, the BAZ1A PHD-DNA interaction has been shown not to be needed for this process <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand <scene name='77/774674/Epe/1'>EPE</scene>, on chains B and D. The ligand is surrounded mainly by hydrophobic residues, as well as aromatic and electrically charged residues. <br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828512 User:Juliet Obi/Sandbox 1 2017-12-02T04:18:53Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand <scene name='77/774674/Epe/1'>EPE</scene>, on chains B and D. The ligand is surrounded mainly by hydrophobic residues, as well as aromatic and electrically charged residues. <br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828511 User:Juliet Obi/Sandbox 1 2017-12-02T04:15:08Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand <scene name='77/774674/Epe/1'>EPE</scene>, on chains B and D.<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828504 User:Juliet Obi/Sandbox 1 2017-12-02T03:22:53Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D.<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=File:5UIY_ligand_sites_mesh_surface.png&diff=2828502 File:5UIY ligand sites mesh surface.png 2017-12-02T03:09:55Z

<p>Juliet Obi: Ligand Interaction domain for 5uiy</p> <hr /> <div>Ligand Interaction domain for 5uiy</div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828501 User:Juliet Obi/Sandbox 1 2017-12-02T03:06:53Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> <br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828497 User:Juliet Obi/Sandbox 1 2017-12-02T02:32:00Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A (PDB entry [[5uiy]])' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> BAZ1A has 4 polypeptide chains and a unique ligand EPE, on chains B and D. <br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828494 User:Juliet Obi/Sandbox 1 2017-12-02T02:20:51Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> <Structure load='5uiy' size='350' frame='true' align='right' caption='Bromodomain Adjacent to Zinc Finger 1A' scene='' /><br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828426 User:Juliet Obi/Sandbox 1 2017-12-01T05:47:59Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <br /> {{STRUCTURE_5uiy| PDB=5uiy | SCENE= }}<br /> <br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828424 User:Juliet Obi/Sandbox 1 2017-12-01T05:20:01Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. This can be attributed to the fact that BAZ1A-PHD lacks the "aromatic cage" as well as other key residues crucial for the recognition of trimethylated lysine <ref>DOI 10.1038/nature04802</ref>. BAZ1A-PHD also lacks acidic residues which particularly recognize unmethylated histone H3 lysine 4 (H3K4) peptides <ref>DOI 10.1038/nature06034</ref>. These information show proof that the PHD finger of BAZ1A might interact with DNA through its other biochemical properties other than the canonical residues which are absent <ref name="s41467"/>.<br /> <br /> The PHD of BAZ1A is structurally similar to its paralog, BAZ1B-PHD and the dual-zinc binding motif characteristic of their PHD fold have been found to be structurally conserved. BAZ1A-PHD is 54% identical and 73% similar to BAZ1B-PHD <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828413 User:Juliet Obi/Sandbox 1 2017-12-01T04:12:09Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAC motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref name="s41467">DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> The PHD finger of bromodomains serves as an epigenetic reader by recognizing the N-terminal histone H3 tail when it is methylated <ref>DOI 10.1016/j.tibs.2011.03.005</ref>. The function of BAZ1A-PHD, N-terminal to its bromodomain, is however unknown <ref name="s41467"/>. <br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828337 User:Juliet Obi/Sandbox 1 2017-11-30T03:37:58Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> === BAZ1A bromodomain histone-ligand recognition ===<br /> <br /> BAZ1A bromodomain as well as BAZ1B a similar bromodomain family member, both have a conserved asparagine "anchor" residue which in functional bromodomains, hydrogen bonds with the carbonyl group of a bound acetyl-lysine ligand and it is crucial for the interaction. This suggests that BAZ1A and BAZ1B could potentially bind an acety-lysine ligand <ref>DOI 10.1016/j.str.2015.08.004</ref>. Also, BAZ1B has an hydrophobic valine "gatekeeper" residue which is found in the binding pockets of several acetyl-lysine binding bromodomains <ref>DOI 10.1016/j.cell.2012.02.013</ref>. Surprisingly, the BAZ1A bromodomain gatekeeper was found to be a non-canonical glutamic acid residue which was found to be compatible with the bromodomain fold through the solving of the crystal structure of BAZ1A bromodomain. The glutamic acid residue introduces a negative charge on the side of the supposed binding pocket of BAZ1A which reduces its affinity for acetylated histone ligands <ref>DOI 10.1038/s41467-017-00866-0</ref>. <br /> <br /> === BAZ1A-PHD binding to DNA ===<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828336 User:Juliet Obi/Sandbox 1 2017-11-30T02:54:26Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features, evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828335 User:Juliet Obi/Sandbox 1 2017-11-30T02:41:18Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function, highlighting the important role BAZ1A has in nervous system development and function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828333 User:Juliet Obi/Sandbox 1 2017-11-30T01:53:25Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B, BAZ2A and BAZ2B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> BAZ1A encodes the chromatin-remodeling factor ACF1, which is a member of the ISWI chromatin remodeling complexes including the ATP-dependent chromatin assembly factor ACF, and the chromatin accessibility complex, CHRAC. BAZ1A (ACF1) has been implicated in a number of functions including chromatin remodeling, assembly and DNA repair. Together with the ISWI subunit, it has been shown to assemble regularly spaced nucleosome arrays in an ATP-dependent manner <ref>PMID:10385622</ref>. BAZ1A functions in certain DNA repair pathways including nucleotide excision repair (NER), non-homologous end-joining (NHEJ) and homologous recombination (HR), through interaction with a catalytic ATPase subunit, SMARCA5 <ref>DOI 10.4161/15384101.2014.956551</ref>. BAZ1A has been shown to have a regulatory function in the transcriptional suppression of vitamin D3 receptor-regulated genes <ref>DOI 10.1210/me.2007-0095</ref>, and in the transcriptional regulation of stress-induced depressive-like behaviors <ref>DOI 10.1038/nm.3939</ref>. A recent study with an identified variant in BAZ1A found that this affects the transcriptional regulatory function of ACF1, thus affecting the expression of genes crucial in vitamin D metabolism, the Wnt signalling pathway, and in proper synaptic function <ref>DOI 10.1002/humu.23034</ref>.<br /> <br /> === DNA binding ===<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828332 User:Juliet Obi/Sandbox 1 2017-11-29T23:53:38Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> === Role in chromatin remodelling ===<br /> <br /> === DNA binding ===<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828325 User:Juliet Obi/Sandbox 1 2017-11-29T19:43:01Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='5uiy' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> <br /> == Role in chromatin remodelling ==<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == DNA binding ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828324 User:Juliet Obi/Sandbox 1 2017-11-29T19:41:09Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> <br /> == Role in chromatin remodelling ==<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == DNA binding ==<br /> <br /> == Medical importance ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828317 User:Juliet Obi/Sandbox 1 2017-11-29T14:02:45Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>. BAZ1A is also known as ACF1, WALp1, hACF1 or WCRF180 <ref>PMID:20033039</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> <br /> == Role in chromatin remodelling ==<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == DNA binding ==<br /> <br /> == Medical implications ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi https://proteopedia.org/index.php?title=User:Juliet_Obi/Sandbox_1&diff=2828299 User:Juliet Obi/Sandbox 1 2017-11-29T13:19:54Z

<p>Juliet Obi: </p> <hr /> <div>==Bromodomain Adjacent to Zinc Finger domain 1A==<br /> <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br /> This is a default text for your page '''Juliet Obi/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> <br /> <br /> == Overview ==<br /> <br /> Bromodomain adjacent to zinc finger 1A (BAZ1A) is a protein in humans encoded by the BAZ1A gene. The protein encoded by the BAZ1A gene contains the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), which is a member of the imitation switch (ISWI) family of chromatin remodeling complexes including BAZ1B. BAZ1A structure contains a plant homeodomain (PHD) zinc finger at the N-terminus, a bromodomain at the C-terminus, a WAKZ motif and a LH (leucine-rich helical domain) motif <ref>DOI 10.1006/geno.1999.6071</ref>.<br /> <br /> == BAZ1A function ==<br /> <br /> <br /> == Role in chromatin remodelling ==<br /> <br /> == Structural features ==<br /> <br /> == Evolution and related structures ==<br /> <br /> == Ligand-interaction domain ==<br /> <br /> == DNA binding ==<br /> <br /> == Medical implications ==<br /> <br /> == References ==<br /> <references/><br /> <br /> This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> </StructureSection></div>

Juliet Obi