5ytk - Revision history

OCA at 08:37, 22 November 2023

OCA — Wed, 22 Nov 2023 08:37:29 GMT

←Older revision		Revision as of 08:37, 22 November 2023
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	==Crystal structure of SIRT3 bound to a leucylated AceCS2==		==Crystal structure of SIRT3 bound to a leucylated AceCS2==
-	<StructureSection load='5ytk' size='340' side='right' caption='[[5ytk]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5ytk' size='340' side='right'caption='[[5ytk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ytk]] is a 10 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=5YTK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YTK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ytk]] is a 10 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=5YTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YTK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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]] 2.7Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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=5ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytk OCA], [~~http~~://pdbe.org/5ytk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ytk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ytk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytk 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=5ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytk OCA], [https://pdbe.org/5ytk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ytk RCSB], [https://www.ebi.ac.uk/pdbsum/5ytk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytk 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/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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ytk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ytk" 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: Homo sapiens]]
-	[[Category: ~~Gong, W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Li, J~~]]	+	[[Category: Gong W]]
-	[[Category: ~~Xu, Y~~]]	+	[[Category: Li J]]
-	[[Category: ~~Dna-dependent deacetylase sirtuin-3]]~~	+	[[Category: Xu Y]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Leucylated acecs2~~]]	+

OCA at 06:02, 3 January 2018

OCA — Wed, 03 Jan 2018 06:02:22 GMT

←Older revision		Revision as of 06:02, 3 January 2018
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	<StructureSection load='5ytk' size='340' side='right' caption='[[5ytk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5ytk' size='340' side='right' caption='[[5ytk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ytk]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ytk]] is a 10 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=5YTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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">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=5ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytk OCA], [http://pdbe.org/5ytk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytk RCSB], [http://www.ebi.ac.uk/pdbsum/5ytk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytk 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=5ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytk OCA], [http://pdbe.org/5ytk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytk RCSB], [http://www.ebi.ac.uk/pdbsum/5ytk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytk 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>		[[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 ==
		+	Amino acids are known regulators of cellular signaling and physiology, but how they are sensed intracellularly is not fully understood. Herein, we report that each aminoacyl-tRNA synthetase (ARS) senses its cognate amino acid sufficiency through catalyzing the formation of lysine aminoacylation (K-AA) on its specific substrate proteins. At physiologic levels, amino acids promote ARSs bound to their substrates and form K-AAs on the varepsilon-amine of lysines in their substrates by producing reactive aminoacyl adenylates. The K-AA marks can be removed by deacetylases, such as SIRT1 and SIRT3, employing the same mechanism as that involved in deacetylation. These dynamically regulated K-AAs transduce signals of their respective amino acids. Reversible leucylation on ras-related GTP-binding protein A/B regulates activity of the mammalian target of rapamycin complex 1. Glutaminylation on apoptosis signal-regulating kinase 1 suppresses apoptosis. We discovered non-canonical functions of ARSs and revealed systematic and functional amino acid sensing and signal transduction networks.
		+
		+	Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations.,He XD, Gong W, Zhang JN, Nie J, Yao CF, Guo FS, Lin Y, Wu XH, Li F, Li J, Sun WC, Wang ED, An YP, Tang HR, Yan GQ, Yang PY, Wei Y, Mao YZ, Lin PC, Zhao JY, Xu Y, Xu W, Zhao SM Cell Metab. 2017 Nov 27. pii: S1550-4131(17)30629-0. doi:, 10.1016/j.cmet.2017.10.015. PMID:29198988<ref>PMID:29198988</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ytk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Gong, W]]		[[Category: Gong, W]]
	[[Category: Li, J]]		[[Category: Li, J]]

OCA at 08:35, 27 December 2017

OCA — Wed, 27 Dec 2017 08:35:02 GMT

←Older revision		Revision as of 08:35, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ytk is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of SIRT3 bound to a leucylated AceCS2==
-		+	<StructureSection load='5ytk' size='340' side='right' caption='[[5ytk]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~Authors~~: Li, J., ~~Gong~~, W., Xu, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ytk]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTK FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of SIRT3 bound~~ to ~~a leucylated AceCS2~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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=5ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytk OCA], [http://pdbe.org/5ytk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytk RCSB], [http://www.ebi.ac.uk/pdbsum/5ytk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytk 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: Gong, W]]
	[[Category: Li, J]]		[[Category: Li, J]]
-	[[Category: Gong, W]]
	[[Category: Xu, Y]]		[[Category: Xu, Y]]
		+	[[Category: Dna-dependent deacetylase sirtuin-3]]
		+	[[Category: Hydrolase]]
		+	[[Category: Leucylated acecs2]]

OCA at 04:48, 20 December 2017

OCA — Wed, 20 Dec 2017 04:48:47 GMT

←Older revision		Revision as of 04:48, 20 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Li, J., Gong, W., Xu, Y.		Authors: Li, J., Gong, W., Xu, Y.

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

OCA — Wed, 29 Nov 2017 04:57:31 GMT

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

←Older revision

Revision as of 04:57, 29 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ytk is ON HOLD Authors: Li, J., Gong, W., Xu, Y. Description: Crystal structure of SIRT3 bound to a leucylated AceCS2 [[Category: Unreleased Struc...

OCA — Wed, 29 Nov 2017 04:57:30 GMT

New page: '''Unreleased structure''' The entry 5ytk is ON HOLD Authors: Li, J., Gong, W., Xu, Y. Description: Crystal structure of SIRT3 bound to a leucylated AceCS2 [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5ytk is ON HOLD

Authors: Li, J., Gong, W., Xu, Y.

Description: Crystal structure of SIRT3 bound to a leucylated AceCS2
[[Category: Unreleased Structures]]
[[Category: Li, J]]
[[Category: Gong, W]]
[[Category: Xu, Y]]