5bwo - Revision history

OCA at 16:05, 8 November 2023

OCA — Wed, 08 Nov 2023 16:05:35 GMT

←Older revision		Revision as of 16:05, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bwo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bwo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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]] 2.376Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [https://pdbe.org/5bwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [https://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo 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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [https://pdbe.org/5bwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [https://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:11, 7 June 2023

OCA — Wed, 07 Jun 2023 06:11:21 GMT

←Older revision		Revision as of 06:11, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5bwo' size='340' side='right'caption='[[5bwo]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='5bwo' size='340' side='right'caption='[[5bwo]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bwo]] 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=5BWO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bwo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwl\|5bwl]], [[5bwn\|5bwn]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [https://pdbe.org/5bwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [https://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIRT3, SIR2L3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [~~http~~://pdbe.org/5bwo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~SIR3_HUMAN SIR3_HUMAN~~]~~] NAD-dependent protein deacetylase~~. ~~Activates mitochondrial target proteins~~, ~~including ACSS1~~, ~~IDH2~~ and ~~GDH by deacetylating key lysine residues~~. ~~Contributes to the regulation~~ of ~~the cellular energy metabolism~~. ~~Important for regulating tissue~~-specific ~~ATP levels~~.~~<ref>PMID:16788062<~~/~~ref> <ref>PMID:18680753</ref> <ref>PMID:18794531</ref>~~ <ref>PMID:~~19535340~~</ref>	+	[https://www.uniprot.org/uniprot/H3C_HUMAN H3C_HUMAN] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.<ref>PMID:21274551</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gai, W~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Jiang, H~~]]	+	[[Category: Gai W]]
-	[[Category: ~~Liu, D~~]]	+	[[Category: Jiang H]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Liu D]]
-	~~[[Category: Peptide-hydrolase complex~~]]	+

OCA at 11:02, 18 March 2020

OCA — Wed, 18 Mar 2020 11:02:50 GMT

←Older revision		Revision as of 11:02, 18 March 2020
Line 1:		Line 1:

	==Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide==		==Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide==
-	<StructureSection load='5bwo' size='340' side='right' caption='[[5bwo]], [[Resolution\|resolution]] 2.38Å' scene=''>	+	<StructureSection load='5bwo' size='340' side='right'caption='[[5bwo]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bwo]] 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=5BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwl\|5bwl]], [[5bwn\|5bwn]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwl\|5bwl]], [[5bwn\|5bwn]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIRT3, SIR2L3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [http://pdbe.org/5bwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [http://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo 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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [http://pdbe.org/5bwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [http://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5bwo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5bwo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gai, W]]		[[Category: Gai, W]]
	[[Category: Jiang, H]]		[[Category: Jiang, H]]

OCA at 19:33, 9 December 2016

OCA — Fri, 09 Dec 2016 19:33:42 GMT

←Older revision		Revision as of 19:33, 9 December 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SIR3_HUMAN SIR3_HUMAN]] NAD-dependent protein deacetylase. Activates mitochondrial target proteins, including ACSS1, IDH2 and GDH by deacetylating key lysine residues. Contributes to the regulation of the cellular energy metabolism. Important for regulating tissue-specific ATP levels.<ref>PMID:16788062</ref> <ref>PMID:18680753</ref> <ref>PMID:18794531</ref> <ref>PMID:19535340</ref>		[[http://www.uniprot.org/uniprot/SIR3_HUMAN SIR3_HUMAN]] NAD-dependent protein deacetylase. Activates mitochondrial target proteins, including ACSS1, IDH2 and GDH by deacetylating key lysine residues. Contributes to the regulation of the cellular energy metabolism. Important for regulating tissue-specific ATP levels.<ref>PMID:16788062</ref> <ref>PMID:18680753</ref> <ref>PMID:18794531</ref> <ref>PMID:19535340</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SIRT1-7 play important roles in many biological processes and age-related diseases. In addition to a NAD(+) -dependent deacetylase activity, they can catalyze several other reactions, including the hydrolysis of long-chain fatty acyl lysine. To study the binding modes of sirtuins to long-chain acyl lysines, we solved the crystal structures of SIRT3 bound to either a H3K9-myristoylated- or a H3K9-palmitoylated peptide. Interaction of SIRT3 with the palmitoyl group led to unfolding of the alpha3-helix. The myristoyl and palmitoyl groups bind to the C-pocket and an allosteric site near the alpha3-helix, respectively. We found that the residues preceding the alpha3-helix determine the size of the C-pocket. The flexibility of the alpha2-alpha3 loop and the plasticity of the alpha3-helix affect the interaction with long-chain acyl lysine.
		+
		+	Crystal structures of SIRT3 reveal that the alpha2-alpha3 loop and alpha3-helix affect the interaction with long-chain acyl lysine.,Gai W, Li H, Jiang H, Long Y, Liu D FEBS Lett. 2016 Sep;590(17):3019-28. doi: 10.1002/1873-3468.12345. Epub 2016 Aug , 24. PMID:27501476<ref>PMID:27501476</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5bwo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:41, 14 July 2016

OCA — Thu, 14 Jul 2016 11:41:55 GMT

←Older revision		Revision as of 11:41, 14 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5bwo is ON HOLD until Paper Publication~~	+	==Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide==
-		+	<StructureSection load='5bwo' size='340' side='right' caption='[[5bwo]], [[Resolution\|resolution]] 2.38Å' scene=''>
-	~~Authors: Gai, W., Jiang, H., Liu, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5bwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWO FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwl\|5bwl]], [[5bwn\|5bwn]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</td></tr>
-	[[~~Category~~: ~~Liu~~, D]]	+	<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=5bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwo OCA], [http://pdbe.org/5bwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwo RCSB], [http://www.ebi.ac.uk/pdbsum/5bwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwo ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SIR3_HUMAN SIR3_HUMAN]] NAD-dependent protein deacetylase. Activates mitochondrial target proteins, including ACSS1, IDH2 and GDH by deacetylating key lysine residues. Contributes to the regulation of the cellular energy metabolism. Important for regulating tissue-specific ATP levels.<ref>PMID:16788062</ref> <ref>PMID:18680753</ref> <ref>PMID:18794531</ref> <ref>PMID:19535340</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gai, W]]		[[Category: Gai, W]]
	[[Category: Jiang, H]]		[[Category: Jiang, H]]
		+	[[Category: Liu, D]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptide-hydrolase complex]]

OCA at 10:54, 1 July 2015

OCA — Wed, 01 Jul 2015 10:54:07 GMT

←Older revision		Revision as of 10:54, 1 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5bwo is ON HOLD	+	The entry 5bwo is ON HOLD until Paper Publication

	Authors: Gai, W., Jiang, H., Liu, D.		Authors: Gai, W., Jiang, H., Liu, D.

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

OCA — Wed, 17 Jun 2015 13:59:56 GMT

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

←Older revision

Revision as of 13:59, 17 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bwo is ON HOLD Authors: Gai, W., Jiang, H., Liu, D. Description: Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide [[Categ...

OCA — Wed, 17 Jun 2015 13:59:54 GMT

New page: '''Unreleased structure''' The entry 5bwo is ON HOLD Authors: Gai, W., Jiang, H., Liu, D. Description: Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide [[Categ...

New page

'''Unreleased structure'''

The entry 5bwo is ON HOLD

Authors: Gai, W., Jiang, H., Liu, D.

Description: Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide
[[Category: Unreleased Structures]]
[[Category: Liu, D]]
[[Category: Gai, W]]
[[Category: Jiang, H]]