5td7 - Revision history

OCA at 12:58, 4 October 2023

2023-10-04T12:58:05Z

←Older revision		Revision as of 12:58, 4 October 2023
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	<StructureSection load='5td7' size='340' side='right'caption='[[5td7]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='5td7' size='340' side='right'caption='[[5td7]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5td7]] 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=5TD7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TD7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5td7]] 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=5TD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TD7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FKS:7-[(3-AMINOPROPYL)AMINO]-1,1,1-TRIFLUOROHEPTANE-2,2-DIOL'>FKS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.85Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hdac10, zgc:55652 ([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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FKS:7-[(3-AMINOPROPYL)AMINO]-1,1,1-TRIFLUOROHEPTANE-2,2-DIOL'>FKS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [~~http~~://pdbe.org/5td7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 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=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [https://pdbe.org/5td7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [https://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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 5td7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5td7" 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: Hai, Y]]	+	[[Category: Hai Y]]
-	[[Category: Porter~~, N J~~]]	+	[[Category: Porter NJ]]
-	[[Category: Shinsky~~, S A]]~~	+	[[Category: Shinsky SA]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:30, 25 December 2019

2019-12-25T12:30:19Z

←Older revision		Revision as of 12:30, 25 December 2019
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	==Crystal structure of histone deacetylase 10==		==Crystal structure of histone deacetylase 10==
-	<StructureSection load='5td7' size='340' side='right' caption='[[5td7]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='5td7' size='340' side='right'caption='[[5td7]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5td7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TD7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TD7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5td7]] 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=5TD7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TD7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FKS:7-[(3-AMINOPROPYL)AMINO]-1,1,1-TRIFLUOROHEPTANE-2,2-DIOL'>FKS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FKS:7-[(3-AMINOPROPYL)AMINO]-1,1,1-TRIFLUOROHEPTANE-2,2-DIOL'>FKS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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, zgc:55652 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [http://pdbe.org/5td7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [http://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 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=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [http://pdbe.org/5td7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [http://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
		+	[[Category: Large Structures]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]
	[[Category: Hai, Y]]		[[Category: Hai, Y]]

OCA at 10:50, 3 August 2017

2017-08-03T10:50:36Z

←Older revision		Revision as of 10:50, 3 August 2017
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	<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=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [http://pdbe.org/5td7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [http://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 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=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [http://pdbe.org/5td7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [http://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cationic polyamines such as spermidine and spermine are critical in all forms of life, as they regulate the function of biological macromolecules. Intracellular polyamine metabolism is regulated by reversible acetylation and dysregulated polyamine metabolism is associated with neoplastic diseases such as colon cancer, prostate cancer and neuroblastoma. Here we report that histone deacetylase 10 (HDAC10) is a robust polyamine deacetylase, using recombinant enzymes from Homo sapiens (human) and Danio rerio (zebrafish). The 2.85 A-resolution crystal structure of zebrafish HDAC10 complexed with a transition-state analogue inhibitor reveals that a glutamate gatekeeper and a sterically constricted active site confer specificity for N8-acetylspermidine hydrolysis and disfavour acetyllysine hydrolysis. Both HDAC10 and spermidine are known to promote cellular survival through autophagy. Accordingly, this work sets a foundation for studying the chemical biology of autophagy through the structure-based design of inhibitors that may also serve as new leads for cancer chemotherapy.
		+
		+	Histone deacetylase 10 structure and molecular function as a polyamine deacetylase.,Hai Y, Shinsky SA, Porter NJ, Christianson DW Nat Commun. 2017 May 18;8:15368. doi: 10.1038/ncomms15368. PMID:28516954<ref>PMID:28516954</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5td7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:48, 24 May 2017

2017-05-24T13:48:49Z

←Older revision		Revision as of 13:48, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5td7 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of histone deacetylase 10==
-		+	<StructureSection load='5td7' size='340' side='right' caption='[[5td7]], [[Resolution\|resolution]] 2.85Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5td7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TD7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TD7 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FKS:7-[(3-AMINOPROPYL)AMINO]-1,1,1-TRIFLUOROHEPTANE-2,2-DIOL'>FKS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5td7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5td7 OCA], [http://pdbe.org/5td7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5td7 RCSB], [http://www.ebi.ac.uk/pdbsum/5td7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5td7 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Christianson, D W]]
		+	[[Category: Hai, Y]]
		+	[[Category: Porter, N J]]
		+	[[Category: Shinsky, S A]]
		+	[[Category: Hydrolase]]

OCA: Protected "5td7" [edit=sysop:move=sysop]

2016-10-03T15:29:08Z

Protected "5td7" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:29, 3 October 2016

OCA: New page: '''Unreleased structure''' The entry 5td7 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-10-03T15:29:07Z

New page: '''Unreleased structure''' The entry 5td7 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5td7 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]