1j1y - Revision history

OCA at 23:40, 27 December 2023

OCA — Wed, 27 Dec 2023 23:40:58 GMT

←Older revision		Revision as of 23:40, 27 December 2023
Line 3:		Line 3:
	<StructureSection load='1j1y' size='340' side='right'caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1j1y' size='340' side='right'caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [https://pdbe.org/1j1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [https://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1y ProSAT], [https://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [https://pdbe.org/1j1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [https://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1y ProSAT], [https://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5SJP3_THET8 Q5SJP3_THET8]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Kunishima, N]]	+	[[Category: Kunishima N]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Kuramitsu S]]
-	[[Category: Miyano, M]]	+	[[Category: Miyano M]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sugahara M]]
-	[[Category: Sugahara, M]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Hot dog fold]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phenylacetic acid degradation]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Thioesterase~~]]	+

OCA at 07:15, 14 April 2021

OCA — Wed, 14 Apr 2021 07:15:49 GMT

←Older revision		Revision as of 07:15, 14 April 2021
Line 3:		Line 3:
	<StructureSection load='1j1y' size='340' side='right'caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1j1y' size='340' side='right'caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [~~http~~://pdbe.org/1j1y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1y ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [https://pdbe.org/1j1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [https://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1y ProSAT], [https://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:08, 10 July 2019

OCA — Wed, 10 Jul 2019 07:08:48 GMT

←Older revision		Revision as of 07:08, 10 July 2019
Line 1:		Line 1:

	==Crystal Structure of PaaI from Thermus thermophilus HB8==		==Crystal Structure of PaaI from Thermus thermophilus HB8==
-	<StructureSection load='1j1y' size='340' side='right' caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1j1y' size='340' side='right'caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
Line 11:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j1/1j1y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j1/1j1y_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>
Line 30:		Line 30:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet8]]		[[Category: Thet8]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 09:40, 4 October 2017

OCA — Wed, 04 Oct 2017 09:40:13 GMT

←Older revision		Revision as of 09:40, 4 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of PaaI from Thermus thermophilus HB8==		==Crystal Structure of PaaI from Thermus thermophilus HB8==
	<StructureSection load='1j1y' size='340' side='right' caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1j1y' size='340' side='right' caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://pdbe.org/1j1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://pdbe.org/1j1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1y ProSAT], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	<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=1j1y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:36, 11 September 2015

OCA — Fri, 11 Sep 2015 14:36:47 GMT

←Older revision		Revision as of 14:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1j1y' size='340' side='right' caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1j1y' size='340' side='right' caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://pdbe.org/1j1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 1j1y" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Thet8]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 11:59, 2 January 2015

OCA — Fri, 02 Jan 2015 11:59:09 GMT

←Older revision		Revision as of 11:59, 2 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Kunishima, N.]]	+	[[Category: Kunishima, N]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Miyano, M.]]	+	[[Category: Miyano, M]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sugahara, M.]]	+	[[Category: Sugahara, M]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Hot dog fold]]		[[Category: Hot dog fold]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phenylacetic acid degradation]]		[[Category: Phenylacetic acid degradation]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Thioesterase]]		[[Category: Thioesterase]]

OCA at 12:41, 28 September 2014

OCA — Sun, 28 Sep 2014 12:41:46 GMT

←Older revision		Revision as of 12:41, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1j1y.~~png\|left~~\|200px]]	+	==Crystal Structure of PaaI from Thermus thermophilus HB8==
		+	<StructureSection load='1j1y' size='340' side='right' caption='[[1j1y]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J1Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<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=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.topsan.org/Proteins/RSGI/1j1y TOPSAN]</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/j1/1j1y_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 ==
		+	Hot dog fold proteins sharing the characteristic "hot dog" fold are known to involve certain coenzyme A binding enzymes with various oligomeric states. In order to elucidate the oligomerization-function relationship of the hot dog fold proteins, crystal structures of the phenylacetate degradation protein PaaI from Thermus thermophilus HB8 (TtPaaI), a tetrameric acyl-CoA thioesterase with the hot dog fold, have been determined and compared with those of other family members. In the liganded crystal forms with coenzyme A derivatives, only two of four intersubunit catalytic pockets of the TtPaaI tetramer are occupied by the ligands. A detailed structural comparison between several liganded and unliganded forms reveals that a subtle rigid-body rearrangement of subunits within 2 degrees upon binding of the first two ligand molecules can induce a strict negative cooperativity to prevent further binding at the remaining two pockets, indicating that the so-called "half-of-the-sites reactivity" of oligomeric enzymes is visualized for the first time. Considering kinetic and mutational analyses together, a possible reaction mechanism of TtPaaI is proposed; one tetramer binds only two acyl-CoA molecules with a novel asymmetric induced-fit mechanism and carries out the hydrolysis according to a base-catalyzed reaction through activation of a water molecule by Asp48. From a structural comparison with other family members, it is concluded that a subgroup of the hot dog fold protein family, referred to as "asymmetric hot dog thioesterases" including medium chain acyl-CoA thioesterase II from Escherichia coli and human thioesterase III, might share the same oligomerization mode and the asymmetric induced-fit mechanism as observed in TtPaaI.

-	~~{{STRUCTURE_1j1y\| PDB=1j1y \| SCENE= }}~~	+	A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI.,Kunishima N, Asada Y, Sugahara M, Ishijima J, Nodake Y, Sugahara M, Miyano M, Kuramitsu S, Yokoyama S, Sugahara M J Mol Biol. 2005 Sep 9;352(1):212-28. PMID:16061252<ref>PMID:16061252</ref>

-	~~===Crystal Structure~~ of ~~PaaI from Thermus thermophilus HB8===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16061252}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1j1y]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016061252<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kunishima, N.]]		[[Category: Kunishima, N.]]

OCA: Protected "1j1y" [edit=sysop:move=sysop]

OCA — Wed, 28 Nov 2012 14:48:46 GMT

Protected "1j1y" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:48, 28 November 2012

OCA at 14:48, 28 November 2012

OCA — Wed, 28 Nov 2012 14:48:43 GMT

←Older revision		Revision as of 14:48, 28 November 2012
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-	{{Seed}}
	[[Image:1j1y.png\|left\|200px]]		[[Image:1j1y.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1j1y", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1j1y\| PDB=1j1y \| SCENE= }}		{{STRUCTURE_1j1y\| PDB=1j1y \| SCENE= }}

	===Crystal Structure of PaaI from Thermus thermophilus HB8===		===Crystal Structure of PaaI from Thermus thermophilus HB8===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16061252}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16061252 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16061252}}		{{ABSTRACT_PUBMED_16061252}}

	==About this Structure==		==About this Structure==
-	~~1J1Y~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA].	+	[[1j1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16061252~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016061252</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kunishima, N.]]		[[Category: Kunishima, N.]]
Line 32:		Line 20:
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S.]]
	[[Category: Hot dog fold]]		[[Category: Hot dog fold]]
		+	[[Category: Hydrolase]]
	[[Category: Phenylacetic acid degradation]]		[[Category: Phenylacetic acid degradation]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
Line 37:		Line 26:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Thioesterase]]		[[Category: Thioesterase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:40:26 2009''

OCA at 22:40, 17 February 2009

OCA — Tue, 17 Feb 2009 22:40:28 GMT

←Older revision		Revision as of 22:40, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI., Kunishima N, Asada Y, Sugahara M, Ishijima J, Nodake Y, Sugahara M, Miyano M, Kuramitsu S, Yokoyama S, Sugahara M, J Mol Biol. 2005 Sep 9;352(1):212-28. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16061252 16061252]~~	+	<ref group="xtra">PMID:16061252</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kunishima, N.]]		[[Category: Kunishima, N.]]
Line 38:		Line 38:
	[[Category: Thioesterase]]		[[Category: Thioesterase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 16~~:13:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:40:26 2009''