1m2k - Revision history

OCA at 18:13, 29 May 2024

OCA — Wed, 29 May 2024 18:13:47 GMT

←Older revision		Revision as of 18:13, 29 May 2024
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2k ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The NAD-dependent histone/protein deacetylase activity of Sir2 (silent information regulator 2) accounts for its diverse biological roles including gene silencing, DNA damage repair, cell cycle regulation, and life span extension. We provide crystallographic evidence that 2'-O-acetyl ADP-ribose is the reaction product that is formed at the active site of Sir2 from the 2.6-A co-crystal structure of 2'-O-acetyl-ADP-ribose and Sir2 from Archaeoglobus fulgidus. In addition, we show that His-116 and Phe-159 play critical roles in the catalysis and substrate recognition. The conserved Ser-24 and Asp-101 contribute to the stability for NAD binding rather than being directly involved in the catalysis. The crystal structures of wild type and mutant derivatives of Sir2, in conjunction with biochemical analyses of the mutants, provide novel insights into the reaction mechanism of Sir2-mediated deacetylation.
		+
		+	Structural basis for the NAD-dependent deacetylase mechanism of Sir2.,Chang JH, Kim HC, Hwang KY, Lee JW, Jackson SP, Bell SD, Cho Y J Biol Chem. 2002 Sep 13;277(37):34489-98. Epub 2002 Jun 28. PMID:12091395<ref>PMID:12091395</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1m2k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:30, 10 April 2024

OCA — Wed, 10 Apr 2024 08:30:37 GMT

←Older revision		Revision as of 08:30, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1m2k' size='340' side='right'caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='1m2k' size='340' side='right'caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arcfl Arcfl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=APR:ADENOSINE~~-~~5-DIPHOSPHORIBOSE'>APR</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]] 1.47Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1m2g\|1m2g]]~~, ~~[[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [https://pdbe.org/1m2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [https://www.ebi.ac.uk/pdbsum/1m2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2k 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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [https://pdbe.org/1m2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [https://www.ebi.ac.uk/pdbsum/1m2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU]] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref>	+	[https://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2k ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The NAD-dependent histone/protein deacetylase activity of Sir2 (silent information regulator 2) accounts for its diverse biological roles including gene silencing, DNA damage repair, cell cycle regulation, and life span extension. We provide crystallographic evidence that 2'-O-acetyl ADP-ribose is the reaction product that is formed at the active site of Sir2 from the 2.6-A co-crystal structure of 2'-O-acetyl-ADP-ribose and Sir2 from Archaeoglobus fulgidus. In addition, we show that His-116 and Phe-159 play critical roles in the catalysis and substrate recognition. The conserved Ser-24 and Asp-101 contribute to the stability for NAD binding rather than being directly involved in the catalysis. The crystal structures of wild type and mutant derivatives of Sir2, in conjunction with biochemical analyses of the mutants, provide novel insights into the reaction mechanism of Sir2-mediated deacetylation.
-
-	Structural basis for the NAD-dependent deacetylase mechanism of Sir2.,Chang JH, Kim HC, Hwang KY, Lee JW, Jackson SP, Bell SD, Cho Y J Biol Chem. 2002 Sep 13;277(37):34489-98. Epub 2002 Jun 28. PMID:12091395<ref>PMID:12091395</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m2k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arcfl~~]]	+	[[Category: Archaeoglobus fulgidus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang, J]]	+	[[Category: Chang J]]
-	[[Category: Cho, Y]]	+	[[Category: Cho Y]]
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Protein-ligand complex~~]]	+

OCA at 06:52, 18 August 2021

OCA — Wed, 18 Aug 2021 06:52:36 GMT

←Older revision		Revision as of 06:52, 18 August 2021
Line 3:		Line 3:
	<StructureSection load='1m2k' size='340' side='right'caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='1m2k' size='340' side='right'caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</div></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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [~~http~~://pdbe.org/1m2k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m2k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2k 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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [https://pdbe.org/1m2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [https://www.ebi.ac.uk/pdbsum/1m2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU]] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref>	+	[[https://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU]] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:21, 13 November 2019

OCA — Wed, 13 Nov 2019 12:21:06 GMT

←Older revision		Revision as of 12:21, 13 November 2019
Line 1:		Line 1:

	==Sir2 homologue F159A mutant-ADP ribose complex==		==Sir2 homologue F159A mutant-ADP ribose complex==
-	<StructureSection load='1m2k' size='340' side='right' caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>	+	<StructureSection load='1m2k' size='340' side='right'caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Arcfl]]		[[Category: Arcfl]]
		+	[[Category: Large Structures]]
	[[Category: Chang, J]]		[[Category: Chang, J]]
	[[Category: Cho, Y]]		[[Category: Cho, Y]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 07:57, 31 January 2018

OCA — Wed, 31 Jan 2018 07:57:08 GMT

←Older revision		Revision as of 07:57, 31 January 2018
Line 1:		Line 1:
		+
	==Sir2 homologue F159A mutant-ADP ribose complex==		==Sir2 homologue F159A mutant-ADP ribose complex==
	<StructureSection load='1m2k' size='340' side='right' caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='1m2k' size='340' side='right' caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://pdbe.org/1m2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum]</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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://pdbe.org/1m2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2k_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2k_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 23:02, 7 February 2016

OCA — Sun, 07 Feb 2016 23:02:13 GMT

←Older revision		Revision as of 23:02, 7 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:40, 10 September 2015

OCA — Thu, 10 Sep 2015 05:40:16 GMT

←Older revision		Revision as of 05:40, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1m2k' size='340' side='right' caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='1m2k' size='340' side='right' caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus Archaeoglobus fulgidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum]</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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://pdbe.org/1m2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1m2k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Archaeoglobus fulgidus~~]]	+	[[Category: Arcfl]]
	[[Category: Chang, J]]		[[Category: Chang, J]]
	[[Category: Cho, Y]]		[[Category: Cho, Y]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 18:48, 24 December 2014

OCA — Wed, 24 Dec 2014 18:48:33 GMT

←Older revision		Revision as of 18:48, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum]</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=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU]] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
-	[[Category: Chang, J.]]	+	[[Category: Chang, J]]
-	[[Category: Cho, Y.]]	+	[[Category: Cho, Y]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 14:30, 28 September 2014

OCA — Sun, 28 Sep 2014 14:30:09 GMT

←Older revision		Revision as of 14:30, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1m2k.~~png~~\|~~left~~\|200px]]	+	==Sir2 homologue F159A mutant-ADP ribose complex==
		+	<StructureSection load='1m2k' size='340' side='right' caption='[[1m2k]], [[Resolution\|resolution]] 1.47Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2K FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2g\|1m2g]], [[1m2h\|1m2h]], [[1m2j\|1m2j]], [[1m2n\|1m2n]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2k RCSB], [http://www.ebi.ac.uk/pdbsum/1m2k PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2k_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The NAD-dependent histone/protein deacetylase activity of Sir2 (silent information regulator 2) accounts for its diverse biological roles including gene silencing, DNA damage repair, cell cycle regulation, and life span extension. We provide crystallographic evidence that 2'-O-acetyl ADP-ribose is the reaction product that is formed at the active site of Sir2 from the 2.6-A co-crystal structure of 2'-O-acetyl-ADP-ribose and Sir2 from Archaeoglobus fulgidus. In addition, we show that His-116 and Phe-159 play critical roles in the catalysis and substrate recognition. The conserved Ser-24 and Asp-101 contribute to the stability for NAD binding rather than being directly involved in the catalysis. The crystal structures of wild type and mutant derivatives of Sir2, in conjunction with biochemical analyses of the mutants, provide novel insights into the reaction mechanism of Sir2-mediated deacetylation.

-	~~{{STRUCTURE_1m2k\| PDB=1m2k \| SCENE= }}~~	+	Structural basis for the NAD-dependent deacetylase mechanism of Sir2.,Chang JH, Kim HC, Hwang KY, Lee JW, Jackson SP, Bell SD, Cho Y J Biol Chem. 2002 Sep 13;277(37):34489-98. Epub 2002 Jun 28. PMID:12091395<ref>PMID:12091395</ref>

-	~~===Sir2 homologue F159A mutant-ADP ribose complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12091395}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1m2k]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1M2K OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012091395<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Chang, J.]]		[[Category: Chang, J.]]

OCA: Protected "1m2k" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 20:01:31 GMT

Protected "1m2k" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:01, 5 December 2012