5zop - Revision history

OCA at 09:02, 22 November 2023

OCA — Wed, 22 Nov 2023 09:02:13 GMT

←Older revision		Revision as of 09:02, 22 November 2023
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	<StructureSection load='5zop' size='340' side='right'caption='[[5zop]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5zop' size='340' side='right'caption='[[5zop]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zop]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZOP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zop]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZOP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=K:POTASSIUM+ION'>K</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.698Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>HDAC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98]~~ </~~span~~></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zop OCA], [https://pdbe.org/5zop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zop RCSB], [https://www.ebi.ac.uk/pdbsum/5zop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zop ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5zop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zop OCA], [~~http~~://pdbe.org/5zop PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zop RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zop PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zop ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[~~http~~://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>	+	[https://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[https://omim.org/entry/600430 600430]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>	+	[https://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5zop" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zop" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histone deacetylase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hwang~~, H J~~]]	+	[[Category: Hwang HJ]]
-	[[Category: Kim~~, J S~~]]	+	[[Category: Kim JS]]
-	[[Category: Park~~, S Y]]~~	+	[[Category: Park SY]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein-peptide complex~~]]	+

OCA at 07:44, 24 April 2019

OCA — Wed, 24 Apr 2019 07:44:10 GMT

←Older revision		Revision as of 07:44, 24 April 2019
Line 1:		Line 1:

	==Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment==		==Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment==
-	<StructureSection load='5zop' size='340' side='right' caption='[[5zop]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5zop' size='340' side='right'caption='[[5zop]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zop]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zop]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zop OCA], [http://pdbe.org/5zop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zop RCSB], [http://www.ebi.ac.uk/pdbsum/5zop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zop ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zop OCA], [http://pdbe.org/5zop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zop RCSB], [http://www.ebi.ac.uk/pdbsum/5zop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zop ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>		[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Modification of chromatin and related transcription factors by histone deacetylases (HDACs) is one of the major strategies for controlling gene expression in eukaryotes. The HDAC domains of class IIa HDACs repress the respective target genes by interacting with the C-terminal region of the silencing mediator for retinoid and thyroid receptor (SMRT) repression domain 3 (SRD3c). However, latent catalytic activity suggests that their roles as deacetylases in gene regulation are unclear. Here, we found that two conserved GSI-containing motifs of SRD3c are critical for HDAC4 binding. Two SMRT peptides including these motifs commonly form a beta-hairpin structure in the cleft and block the catalytic entry site of HDAC4. They interact mainly with class IIa HDAC-specific residues of HDAC4 in a closed conformation. Structure-guided mutagenesis confirmed critical interactions between the SMRT peptides and HDAC4 and -5 as well as the contribution of the Arg1369 residue in the first motif for optimal binding to the two HDACs. These results indicate that SMRT binding does not activate the cryptic deacetylase activity of HDAC4 and explain how class IIa HDACs and the SMRT-HDAC3 complex are coordinated during gene regulation.
		+
		+	Structural basis of the specific interaction of SMRT corepressor with histone deacetylase 4.,Park SY, Kim GS, Hwang HJ, Nam TH, Park HS, Song J, Jang TH, Lee YC, Kim JS Nucleic Acids Res. 2018 Oct 13. pii: 5128926. doi: 10.1093/nar/gky926. PMID:30321390<ref>PMID:30321390</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zop" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Hwang, H J]]		[[Category: Hwang, H J]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]

OCA at 08:01, 10 October 2018

OCA — Wed, 10 Oct 2018 08:01:03 GMT

←Older revision		Revision as of 08:01, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zop is ~~ON HOLD until Apr 13 2020~~	+	==Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment==
-		+	<StructureSection load='5zop' size='340' side='right' caption='[[5zop]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~Authors~~: ~~Park~~, S.Y., ~~Hwang~~, H.J., ~~Kim~~, J.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zop]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOP FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~histone deacetylase 4~~ (~~HDAC4~~) in ~~complex with~~ a ~~SMRT corepressor SP2 fragment~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>
-	[[Category: Kim, J.S]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zop OCA], [http://pdbe.org/5zop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zop RCSB], [http://www.ebi.ac.uk/pdbsum/5zop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zop ProSAT]</span></td></tr>
-	[[Category: Park, S.Y]]	+	</table>
-	[[Category: ~~Hwang, H.J~~]]	+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[http://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone deacetylase]]
		+	[[Category: Hwang, H J]]
		+	[[Category: Kim, J S]]
		+	[[Category: Park, S Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein-peptide complex]]

OCA at 06:32, 2 May 2018

OCA — Wed, 02 May 2018 06:32:54 GMT

←Older revision		Revision as of 06:32, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zop is ON HOLD	+	The entry 5zop is ON HOLD until Apr 13 2020

	Authors: Park, S.Y., Hwang, H.J., Kim, J.S.		Authors: Park, S.Y., Hwang, H.J., Kim, J.S.

OCA: Protected "5zop" [edit=sysop:move=sysop]

OCA — Wed, 25 Apr 2018 03:51:35 GMT

Protected "5zop" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:51, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zop is ON HOLD Authors: Park, S.Y., Hwang, H.J., Kim, J.S. Description: Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT ...

OCA — Wed, 25 Apr 2018 03:51:34 GMT

New page: '''Unreleased structure''' The entry 5zop is ON HOLD Authors: Park, S.Y., Hwang, H.J., Kim, J.S. Description: Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT ...

New page

'''Unreleased structure'''

The entry 5zop is ON HOLD

Authors: Park, S.Y., Hwang, H.J., Kim, J.S.

Description: Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment
[[Category: Unreleased Structures]]
[[Category: Kim, J.S]]
[[Category: Park, S.Y]]
[[Category: Hwang, H.J]]