1wka - Revision history

OCA at 07:56, 25 October 2023

OCA — Wed, 25 Oct 2023 07:56:29 GMT

←Older revision		Revision as of 07:56, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1wka' size='340' side='right'caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1wka' size='340' side='right'caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKA FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1wk9\|1wk9]]</div></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~~='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Valine~~-~~-tRNA_ligase Valine--tRNA ligase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.~~1.~~1.9 6.1.1.9] </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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [https://pdbe.org/1wka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [https://www.ebi.ac.uk/pdbsum/1wka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wka ProSAT], [https://www.topsan.org/Proteins/RSGI/1wka 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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [https://pdbe.org/1wka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [https://www.ebi.ac.uk/pdbsum/1wka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wka ProSAT], [https://www.topsan.org/Proteins/RSGI/1wka TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]	+	[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Valine--tRNA ligase~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Fukunaga, R]]	+	[[Category: Fukunaga R]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Amino acid]]~~	+
-	~~[[Category: Cp1]]~~	+
-	~~[[Category: Editing]]~~	+
-	~~[[Category: Fidelity]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Thermus thrmophilus]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Valyl-trna synthetase~~]]	+

OCA at 16:20, 27 October 2021

OCA — Wed, 27 Oct 2021 16:20:23 GMT

←Older revision		Revision as of 16:20, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1wka' size='340' side='right'caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1wka' size='340' side='right'caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKA FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wk9\|1wk9]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [~~http~~://pdbe.org/1wka PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wka PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wka ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1wka 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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [https://pdbe.org/1wka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [https://www.ebi.ac.uk/pdbsum/1wka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wka ProSAT], [https://www.topsan.org/Proteins/RSGI/1wka TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]	+	[[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 18:05, 22 January 2020

OCA — Wed, 22 Jan 2020 18:05:07 GMT

←Older revision		Revision as of 18:05, 22 January 2020
Line 1:		Line 1:

	==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain==		==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain==
-	<StructureSection load='1wka' size='340' side='right' caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1wka' size='340' side='right'caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]

OCA at 16:45, 11 April 2018

OCA — Wed, 11 Apr 2018 16:45:02 GMT

←Older revision		Revision as of 16:45, 11 April 2018
Line 1:		Line 1:
		+
	==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain==		==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain==
	<StructureSection load='1wka' size='340' side='right' caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1wka' size='340' side='right' caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://pdbe.org/1wka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://www.topsan.org/Proteins/RSGI/1wka 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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://pdbe.org/1wka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wka ProSAT], [http://www.topsan.org/Proteins/RSGI/1wka TOPSAN]</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/wk/1wka_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wk/1wka_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>
	</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=1wka ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:28, 11 September 2015

OCA — Fri, 11 Sep 2015 16:28:00 GMT

←Older revision		Revision as of 16:28, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1wka' size='340' side='right' caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1wka' size='340' side='right' caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wka]] is a 1 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=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://www.topsan.org/Proteins/RSGI/1wka 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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://pdbe.org/1wka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://www.topsan.org/Proteins/RSGI/1wka TOPSAN]</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 1wka" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]

OCA at 19:00, 25 December 2014

OCA — Thu, 25 Dec 2014 19:00:24 GMT

←Older revision		Revision as of 19:00, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wka]] is a 1 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=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wka]] is a 1 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=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://www.topsan.org/Proteins/RSGI/1wka 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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://www.topsan.org/Proteins/RSGI/1wka TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]
-	[[Category: Fukunaga, R.]]	+	[[Category: Fukunaga, R]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Amino acid]]		[[Category: Amino acid]]
	[[Category: Cp1]]		[[Category: Cp1]]
Line 42:		Line 44:
	[[Category: Fidelity]]		[[Category: Fidelity]]
	[[Category: Ligase]]		[[Category: Ligase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Thermus thrmophilus]]		[[Category: Thermus thrmophilus]]
	[[Category: Translation]]		[[Category: Translation]]
	[[Category: Valyl-trna synthetase]]		[[Category: Valyl-trna synthetase]]

OCA at 00:14, 29 September 2014

OCA — Mon, 29 Sep 2014 00:14:37 GMT

←Older revision		Revision as of 00:14, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wka.~~png~~\|~~left~~\|200px]]	+	==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain==
		+	<StructureSection load='1wka' size='340' side='right' caption='[[1wka]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wka]] is a 1 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=1WKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wk9\|1wk9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></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=1wka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wka RCSB], [http://www.ebi.ac.uk/pdbsum/1wka PDBsum], [http://www.topsan.org/Proteins/RSGI/1wka 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/wk/1wka_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 editing domain of valyl-tRNA synthetase (ValRS) is known to deacylate, or edit, misformed Thr-tRNA(Val) (post-transfer editing). Here, we determined the 1.7-Angstroms resolution crystal structure of the Thermus thermophilus ValRS editing domain. A comparison of the structure with the previously reported tRNA complex structure revealed conformational changes of the editing domain upon accommodation of the terminal A76; the "GTG loop" moves to expand the pocket, and the side chain of Phe-264 on the GTG loop rotates to interact with the A76 adenine ring. If these conformational changes did not occur, then C75 and A76 of the tRNA would clash with Phe-264. To elucidate the mechanism of the threonine side-chain recognition, we determined the crystal structure of the editing domain bound with [N-(L-threonyl)-sulfamoyl]adenosine at 1.7-Angstroms resolution. The gamma-OH of the threonyl moiety is recognized by the Lys-270, Thr-272, and Asp-279 side chains, which may reject the cognate valyl moiety. Accordingly, ValRS mutants with an Ala substitution for Lys-270 or Asp-279 synthesized significant amounts of Thr-tRNA(Val). The misproduced Thr-tRNA(Val) was hydrolyzed efficiently by the wild-type ValRS, but this post-transfer editing activity was drastically impaired by the Ala substitutions for Lys-270 and Asp-279 and was also decreased by those for Arg-216, Phe-264, and Thr-272. These results indicate that the threonyl moiety and A76 of Thr-tRNA(Val) are recognized by the Lys-270, Thr-272, and Asp-279 side chains and by the Phe-264 side chain, respectively, of the ValRS editing domain.

-	~~{{STRUCTURE_1wka\| PDB=1wka \| SCENE= }}~~	+	Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain.,Fukunaga R, Yokoyama S J Biol Chem. 2005 Aug 19;280(33):29937-45. Epub 2005 Jun 21. PMID:15970591<ref>PMID:15970591</ref>

-	~~===Structural basis for non-cognate amino acid discrimination by~~ the ~~valyl-tRNA synthetase editing domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15970591}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1wka]] is a 1 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=1WKA OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015970591<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]

OCA at 20:17, 20 October 2012

OCA — Sat, 20 Oct 2012 20:17:43 GMT

←Older revision		Revision as of 20:17, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1wka]] is a 1 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ 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=1WKA OCA].	+	[[1wka]] is a 1 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=1WKA OCA].

	==See Also==		==See Also==

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

OCA — Fri, 27 Jul 2012 10:01:07 GMT

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

←Older revision

Revision as of 10:01, 27 July 2012

OCA at 10:01, 27 July 2012

OCA — Fri, 27 Jul 2012 10:01:04 GMT

←Older revision		Revision as of 10:01, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wka.png\|left\|200px]]		[[Image:1wka.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wka", 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.
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	{{STRUCTURE_1wka\| PDB=1wka \| SCENE= }}		{{STRUCTURE_1wka\| PDB=1wka \| SCENE= }}

	===Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain===		===Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15970591}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15970591 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15970591}}		{{ABSTRACT_PUBMED_15970591}}

	==About this Structure==		==About this Structure==
-	~~1WKA~~ is a 1 chain structure of 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=1WKA OCA].	+	[[1wka]] is a 1 chain structure of [[Aminoacyl tRNA Synthetase]] 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=1WKA OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15970591~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015970591</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]
Line 33:		Line 24:
	[[Category: Editing]]		[[Category: Editing]]
	[[Category: Fidelity]]		[[Category: Fidelity]]
		+	[[Category: Ligase]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
Line 39:		Line 31:
	[[Category: Translation]]		[[Category: Translation]]
	[[Category: Valyl-trna synthetase]]		[[Category: Valyl-trna synthetase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:45:40 2009''