1wny - Revision history

OCA at 13:32, 13 March 2024

OCA — Wed, 13 Mar 2024 13:32:53 GMT

←Older revision		Revision as of 13:32, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wny' size='340' side='right'caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wny' size='340' side='right'caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WNY 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;'>[[1wnz\|1wnz]]</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]] 1.6Å</td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isoleucine~~-~~-tRNA_ligase Isoleucine--tRNA ligase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.~~1.~~1.5~~ 6~~.1.1.5] </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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [https://pdbe.org/1wny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [https://www.ebi.ac.uk/pdbsum/1wny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wny ProSAT], [https://www.topsan.org/Proteins/RSGI/1wny 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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [https://pdbe.org/1wny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [https://www.ebi.ac.uk/pdbsum/1wny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wny ProSAT], [https://www.topsan.org/Proteins/RSGI/1wny TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYI_THET8 SYI_THET8]] Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity).[HAMAP-Rule:MF_02003]	+	[https://www.uniprot.org/uniprot/SYI_THET8 SYI_THET8] Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity).[HAMAP-Rule:MF_02003]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=1wny 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=1wny ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In the present study, we determined the crystal structures of the Thermus thermophilus IleRS editing domain complexed with the substrate analogues in the pre and post-transfer modes, both at 1.7 A resolution. The active site accommodates the two analogues differently, with the valine side-chain rotated by about 120 degrees and the adenosine moiety oriented upside down. The substrate-binding pocket adjusts to the adenosine-monophosphate and adenosine moieties in the pre and post-transfer modes, respectively, by flipping the Trp227 side-chain by about 180 degrees . The substrate recognition mechanisms of IleRS are characterized by the active-site rearrangement between the two editing modes, and therefore differ from those of the homologous valyl and leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer mode is predominant. Both modes of editing activities were reduced by replacements of Trp227 with Ala, Val, Leu, and His, but not by those with Phe and Tyr, indicating that the aromatic ring of Trp227 is important for the substrate recognition. In both editing modes, Thr233 and His319 recognize the substrate valine side-chain, regardless of the valine side-chain rotation, and reject the isoleucine side-chain. The T233A and H319A mutants have detectable editing activities against the cognate isoleucine.
-
-	Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase.,Fukunaga R, Yokoyama S J Mol Biol. 2006 Jun 16;359(4):901-12. Epub 2006 Apr 25. PMID:16697013<ref>PMID:16697013</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wny" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]		*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: Isoleucine--tRNA ligase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fukunaga, R~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Fukunaga R]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 16:23, 27 October 2021

OCA — Wed, 27 Oct 2021 16:23:04 GMT

←Older revision		Revision as of 16:23, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1wny' size='340' side='right'caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wny' size='340' side='right'caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WNY FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</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;'>[[1wnz\|1wnz]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [~~http~~://pdbe.org/1wny PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wny PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wny ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1wny 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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [https://pdbe.org/1wny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [https://www.ebi.ac.uk/pdbsum/1wny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wny ProSAT], [https://www.topsan.org/Proteins/RSGI/1wny TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYI_THET8 SYI_THET8]] Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity).[HAMAP-Rule:MF_02003]	+	[[https://www.uniprot.org/uniprot/SYI_THET8 SYI_THET8]] Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity).[HAMAP-Rule:MF_02003]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 17:28, 22 January 2020

OCA — Wed, 22 Jan 2020 17:28:08 GMT

←Older revision		Revision as of 17:28, 22 January 2020
Line 1:		Line 1:

	==Isoleucyl-tRNA synthetase editing domain==		==Isoleucyl-tRNA synthetase editing domain==
-	<StructureSection load='1wny' size='340' side='right' caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1wny' size='340' side='right'caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY 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 38:		Line 38:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
		+	[[Category: Large Structures]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 16:14, 11 April 2018

OCA — Wed, 11 Apr 2018 16:14:00 GMT

←Older revision		Revision as of 16:14, 11 April 2018
Line 1:		Line 1:
		+
	==Isoleucyl-tRNA synthetase editing domain==		==Isoleucyl-tRNA synthetase editing domain==
	<StructureSection load='1wny' size='340' side='right' caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wny' size='340' side='right' caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://pdbe.org/1wny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://www.topsan.org/Proteins/RSGI/1wny 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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://pdbe.org/1wny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wny ProSAT], [http://www.topsan.org/Proteins/RSGI/1wny 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/wn/1wny_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wn/1wny_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=1wny ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:07, 11 September 2015

OCA — Fri, 11 Sep 2015 12:07:10 GMT

←Older revision		Revision as of 12:07, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1wny' size='340' side='right' caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wny' size='340' side='right' caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wny]] 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wny]] is a 2 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://www.topsan.org/Proteins/RSGI/1wny 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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://pdbe.org/1wny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://www.topsan.org/Proteins/RSGI/1wny 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 1wny" style="background-color:#fffaf0;"></div>

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

OCA at 16:14, 25 December 2014

OCA — Thu, 25 Dec 2014 16:14:27 GMT

←Older revision		Revision as of 16:14, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wny]] 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wny]] 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://www.topsan.org/Proteins/RSGI/1wny 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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://www.topsan.org/Proteins/RSGI/1wny TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYI_THET8 SYI_THET8]] Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity).[HAMAP-Rule:MF_02003]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Fukunaga, R.]]	+	[[Category: Fukunaga, R]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 20:59, 28 September 2014

OCA — Sun, 28 Sep 2014 20:59:12 GMT

←Older revision		Revision as of 20:59, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wny.~~png~~\|~~left~~\|200px]]	+	==Isoleucyl-tRNA synthetase editing domain==
		+	<StructureSection load='1wny' size='340' side='right' caption='[[1wny]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wny]] 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=1WNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnz\|1wnz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </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=1wny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wny RCSB], [http://www.ebi.ac.uk/pdbsum/1wny PDBsum], [http://www.topsan.org/Proteins/RSGI/1wny 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/wn/1wny_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 ==
		+	In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In the present study, we determined the crystal structures of the Thermus thermophilus IleRS editing domain complexed with the substrate analogues in the pre and post-transfer modes, both at 1.7 A resolution. The active site accommodates the two analogues differently, with the valine side-chain rotated by about 120 degrees and the adenosine moiety oriented upside down. The substrate-binding pocket adjusts to the adenosine-monophosphate and adenosine moieties in the pre and post-transfer modes, respectively, by flipping the Trp227 side-chain by about 180 degrees . The substrate recognition mechanisms of IleRS are characterized by the active-site rearrangement between the two editing modes, and therefore differ from those of the homologous valyl and leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer mode is predominant. Both modes of editing activities were reduced by replacements of Trp227 with Ala, Val, Leu, and His, but not by those with Phe and Tyr, indicating that the aromatic ring of Trp227 is important for the substrate recognition. In both editing modes, Thr233 and His319 recognize the substrate valine side-chain, regardless of the valine side-chain rotation, and reject the isoleucine side-chain. The T233A and H319A mutants have detectable editing activities against the cognate isoleucine.

-	~~{{STRUCTURE_1wny\| PDB=1wny \| SCENE= }}~~	+	Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase.,Fukunaga R, Yokoyama S J Mol Biol. 2006 Jun 16;359(4):901-12. Epub 2006 Apr 25. PMID:16697013<ref>PMID:16697013</ref>

-	~~===Isoleucyl-tRNA synthetase editing domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16697013}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1wny]] 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=1WNY OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016697013<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 18:46, 20 October 2012

OCA — Sat, 20 Oct 2012 18:46:43 GMT

←Older revision		Revision as of 18:46, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1wny]] is a 2 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=1WNY OCA].	+	[[1wny]] 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=1WNY OCA].

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

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

OCA — Fri, 27 Jul 2012 05:12:03 GMT

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

←Older revision

Revision as of 05:12, 27 July 2012

OCA at 05:12, 27 July 2012

OCA — Fri, 27 Jul 2012 05:12:02 GMT

←Older revision		Revision as of 05:12, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wny.png\|left\|200px]]		[[Image:1wny.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wny", 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_1wny\| PDB=1wny \| SCENE= }}		{{STRUCTURE_1wny\| PDB=1wny \| SCENE= }}

	===Isoleucyl-tRNA synthetase editing domain===		===Isoleucyl-tRNA synthetase editing domain===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16697013}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16697013 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16697013}}		{{ABSTRACT_PUBMED_16697013}}

	==About this Structure==		==About this Structure==
-	~~1WNY~~ 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=1WNY OCA].	+	[[1wny]] is a 2 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=1WNY OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16697013~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016697013</ref><references group="xtra"/>
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 35:		Line 26:
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:27:48 2009''