6wdy - Revision history

OCA at 14:22, 18 October 2023

OCA — Wed, 18 Oct 2023 14:22:25 GMT

←Older revision		Revision as of 14:22, 18 October 2023
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	<StructureSection load='6wdy' size='340' side='right'caption='[[6wdy]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6wdy' size='340' side='right'caption='[[6wdy]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6wdy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WDY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WDY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wdy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WDY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TWP:N-hydroxy-4-[(1H-indol-1-yl)methyl]benzamide'>TWP</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]] 2.65Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hdac10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TWP:N-hydroxy-4-[(1H-indol-1-yl)methyl]benzamide'>TWP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6wdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdy OCA], [~~http~~://pdbe.org/6wdy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wdy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wdy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdy ProSAT]</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=6wdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdy OCA], [https://pdbe.org/6wdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wdy RCSB], [https://www.ebi.ac.uk/pdbsum/6wdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HDA10_DANRE HDA10_DANRE]] Polyamine deacetylase (PDAC), which acts preferentially on N(8)-acetylspermidine, and also on acetylcadaverine and acetylputrescine (PubMed:28516954). Exhibits attenuated catalytic activity toward N(1),N(8)-diacetylspermidine and very low activity, if any, toward N(1)-acetylspermidine (PubMed:28516954). Has a very weak lysine deacetylase, if any (PubMed:28516954).<ref>PMID:28516954</ref>	+	[https://www.uniprot.org/uniprot/HDA10_DANRE HDA10_DANRE] Polyamine deacetylase (PDAC), which acts preferentially on N(8)-acetylspermidine, and also on acetylcadaverine and acetylputrescine (PubMed:28516954). Exhibits attenuated catalytic activity toward N(1),N(8)-diacetylspermidine and very low activity, if any, toward N(1)-acetylspermidine (PubMed:28516954). Has a very weak lysine deacetylase, if any (PubMed:28516954).<ref>PMID:28516954</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christianson~~, D W~~]]	+	[[Category: Christianson DW]]
-	[[Category: Herbst-Gervasoni~~, C J]]~~	+	[[Category: Herbst-Gervasoni CJ]]
-	~~[[Category: Histone deacetylase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 07:09, 2 September 2020

OCA — Wed, 02 Sep 2020 07:09:01 GMT

←Older revision		Revision as of 07:09, 2 September 2020
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	</div>		</div>
	<div class="pdbe-citations 6wdy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6wdy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:38, 29 July 2020

OCA — Wed, 29 Jul 2020 11:38:10 GMT

←Older revision		Revision as of 11:38, 29 July 2020
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	==Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole Phenylhydroxamate Inhibitor==		==Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole Phenylhydroxamate Inhibitor==
-	<StructureSection load='6wdy' size='340' side='right'caption='[[6wdy]]' scene=''>	+	<StructureSection load='6wdy' size='340' side='right'caption='[[6wdy]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WDY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WDY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wdy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WDY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WDY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdy OCA], [http://pdbe.org/6wdy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wdy RCSB], [http://www.ebi.ac.uk/pdbsum/6wdy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdy ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TWP:N-hydroxy-4-[(1H-indol-1-yl)methyl]benzamide'>TWP</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">hdac10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdy OCA], [http://pdbe.org/6wdy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wdy RCSB], [http://www.ebi.ac.uk/pdbsum/6wdy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HDA10_DANRE HDA10_DANRE]] Polyamine deacetylase (PDAC), which acts preferentially on N(8)-acetylspermidine, and also on acetylcadaverine and acetylputrescine (PubMed:28516954). Exhibits attenuated catalytic activity toward N(1),N(8)-diacetylspermidine and very low activity, if any, toward N(1)-acetylspermidine (PubMed:28516954). Has a very weak lysine deacetylase, if any (PubMed:28516954).<ref>PMID:28516954</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cytosolic class IIb histone deacetylase HDAC10 is an emerging target for drug design. As an inducer of autophagy, its selective inhibition suppresses the autophagic response that otherwise attenuates the efficacy of cytotoxic cancer chemotherapy drugs. HDAC10 is a zinc-dependent polyamine deacetylase exhibiting maximal catalytic activity against N(8)-acetylspermidine. As revealed in the structure of Danio rerio (zebrafish) HDAC10, two conserved structural motifs direct this narrow substrate specificity: a 310 helix containing the P(E,A)CE motif that sterically constricts the active site and an electrostatic "gatekeeper," E274, that confers selectivity for cationic polyamine substrates. To accelerate drug design efforts targeting human HDAC10, we now report the preparation of "humanized" zebrafish HDAC10 in which two amino acid substitutions, A24E and D94A, yield an active site contour more similar to that of human HDAC10. X-ray crystal structures of this HDAC10 variant complexed with Tubastatin A and indole analogues bearing pendant tertiary amines reveal that inhibitors capable of hydrogen bonding with gatekeeper E274 exhibit high affinity and selectivity for HDAC10 over HDAC6 (the other class IIb isozyme). Moreover, these structures reveal that the P(E,A)CE motif helix can shift by up to 2 A to accommodate the binding of bulky inhibitors. Thus, slender polyamine-like inhibitor structures are not exclusively required for selective, high affinity binding to HDAC10. Indeed, the flexibility of the P(E,A)CE motif helix could conceivably enable the binding of certain protein substrates.
		+
		+	Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.,Herbst-Gervasoni CJ, Steimbach RR, Morgen M, Miller AK, Christianson DW ACS Chem Biol. 2020 Jul 23. doi: 10.1021/acschembio.0c00362. PMID:32659072<ref>PMID:32659072</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wdy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christianson DW]]	+	[[Category: Christianson, D W]]
-	[[Category: Herbst-Gervasoni CJ]]	+	[[Category: Herbst-Gervasoni, C J]]
		+	[[Category: Histone deacetylase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 10:53, 22 July 2020

OCA — Wed, 22 Jul 2020 10:53:29 GMT

←Older revision		Revision as of 10:53, 22 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6wdy ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole Phenylhydroxamate Inhibitor==
-		+	<StructureSection load='6wdy' size='340' side='right'caption='[[6wdy]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WDY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WDY FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdy OCA], [http://pdbe.org/6wdy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wdy RCSB], [http://www.ebi.ac.uk/pdbsum/6wdy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Christianson DW]]
		+	[[Category: Herbst-Gervasoni CJ]]

OCA at 05:21, 15 April 2020

OCA — Wed, 15 Apr 2020 05:21:13 GMT

←Older revision		Revision as of 05:21, 15 April 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6wdy is ON HOLD	+	The entry 6wdy is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6wdy" [edit=sysop:move=sysop]

OCA — Wed, 08 Apr 2020 05:39:13 GMT

Protected "6wdy" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:39, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 6wdy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Apr 2020 05:39:11 GMT

New page: '''Unreleased structure''' The entry 6wdy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6wdy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]