6uim - Revision history

OCA at 07:52, 11 October 2023

OCA — Wed, 11 Oct 2023 07:52:08 GMT

←Older revision		Revision as of 07:52, 11 October 2023
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	<StructureSection load='6uim' size='340' side='right'caption='[[6uim]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6uim' size='340' side='right'caption='[[6uim]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6uim]] 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=6UIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uim]] 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=6UIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UIM 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=Q7Y:7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one'>Q7Y</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]] 2.75Å</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=6uim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uim OCA], [~~http~~://pdbe.org/6uim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uim ProSAT]</span></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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=Q7Y:7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one'>Q7Y</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'>[https://proteopedia.org/fgij/fg.htm?mol=6uim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uim OCA], [https://pdbe.org/6uim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uim RCSB], [https://www.ebi.ac.uk/pdbsum/6uim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uim 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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	</div>		</div>
	<div class="pdbe-citations 6uim" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6uim" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__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 13:22, 18 December 2019

OCA — Wed, 18 Dec 2019 13:22:52 GMT

←Older revision		Revision as of 13:22, 18 December 2019
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	<StructureSection load='6uim' size='340' side='right'caption='[[6uim]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6uim' size='340' side='right'caption='[[6uim]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6uim]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uim]] 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=6UIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UIM 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=Q7Y:7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one'>Q7Y</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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=Q7Y:7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one'>Q7Y</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6uim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uim OCA], [http://pdbe.org/6uim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uim RCSB], [http://www.ebi.ac.uk/pdbsum/6uim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uim 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=6uim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uim OCA], [http://pdbe.org/6uim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uim RCSB], [http://www.ebi.ac.uk/pdbsum/6uim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uim ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]

OCA at 08:24, 4 December 2019

OCA — Wed, 04 Dec 2019 08:24:22 GMT

←Older revision		Revision as of 08:24, 4 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6uim is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-{[(3-aminopropyl)amino]-2-oxoheptyl} thioacetate==
		+	<StructureSection load='6uim' size='340' side='right'caption='[[6uim]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6uim]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UIM 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=Q7Y:7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one'>Q7Y</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6uim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uim OCA], [http://pdbe.org/6uim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uim RCSB], [http://www.ebi.ac.uk/pdbsum/6uim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uim ProSAT]</span></td></tr>
		+	</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 ==
		+	Eukaryotic histone deacetylase 10 (HDAC10) is a Zn(2+)-dependent hydrolase that exhibits catalytic specificity for the hydrolysis of the polyamine N(8)-acetylspermidine. The recently determined crystal structure of HDAC10 from Danio rerio (zebrafish) reveals a narrow active site cleft and a negatively charged "gatekeeper" (E274) that favors the binding of the slender cationic substrate. Because HDAC10 expression is upregulated in advanced-stage neuroblastoma and induces autophagy, the selective inhibition of HDAC10 suppresses the autophagic response and renders cancer cells more susceptible to cytotoxic chemotherapeutic drugs. Here, we describe X-ray crystal structures of zebrafish HDAC10 complexed with eight different analogues of N(8)-acetylspermidine. These analogues contain different Zn(2+)-binding groups, such as hydroxamate, thiolate, and the tetrahedral gem-diolate resulting from the addition of a Zn(2+)-bound water molecule to a ketone carbonyl group. Notably, the chemistry that accompanies the binding of ketonic substrate analogues is identical to the chemistry involved in the first step of catalysis, i.e., nucleophilic attack of a Zn(2+)-bound water molecule at the scissile carbonyl group of N(8)-acetylspermidine. The most potent inhibitor studied contains a thiolate Zn(2+)-binding group. These structures reveal interesting geometric changes in the metal coordination polyhedron that accommodate inhibitor binding. Additional interactions in the active site highlight features contributing to substrate specificity. These interactions are likely to contribute to inhibitor binding selectivity and will inform the future design of compounds selective for HDAC10 inhibition.

-	~~Authors~~:	+	Binding of N(8)-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation.,Herbst-Gervasoni CJ, Christianson DW Biochemistry. 2019 Dec 2. doi: 10.1021/acs.biochem.9b00906. PMID:31746596<ref>PMID:31746596</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6uim" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Christianson, D W]]
		+	[[Category: Herbst-Gervasoni, C J]]
		+	[[Category: Histone deacetylase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 04:33, 16 October 2019

OCA — Wed, 16 Oct 2019 04:33:50 GMT

←Older revision		Revision as of 04:33, 16 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Thu, 10 Oct 2019 04:00:23 GMT

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

←Older revision

Revision as of 04:00, 10 October 2019

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

OCA — Thu, 10 Oct 2019 04:00:21 GMT

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

New page

'''Unreleased structure'''

The entry 6uim is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]