1udz - Revision history

OCA at 06:16, 3 April 2024

OCA — Wed, 03 Apr 2024 06:16:33 GMT

←Older revision		Revision as of 06:16, 3 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>
-	</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [https://pdbe.org/1udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [https://www.ebi.ac.uk/pdbsum/1udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [https://www.topsan.org/Proteins/RSGI/1udz TOPSAN]</span></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]] 1.8Å</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [https://pdbe.org/1udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [https://www.ebi.ac.uk/pdbsum/1udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [https://www.topsan.org/Proteins/RSGI/1udz TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		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=1udz 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=1udz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Isoleucyl-tRNA synthetase (IleRS) links tRNA(Ile) with not only its cognate isoleucine but also the nearly cognate valine. The CP1 domain of IleRS deacylates, or edits, the mischarged Val-tRNA(Ile). We determined the crystal structures of the Thermus thermophilus IleRS CP1 domain alone, and in its complex with valine at 1.8- and 2.0-A resolutions, respectively. In the complex structure, the Asp(328) residue, which was shown to be critical for the editing reaction against Val-tRNA(Ile) by a previous mutational analysis, recognizes the valine NH(3)(+) group. The valine side chain binding pocket is only large enough to accommodate valine, and the placement of an isoleucine model in this location revealed that the additional methylene group of isoleucine would clash with His(319). The H319A mutant of Escherichia coli IleRS reportedly deacylates the cognate Ile-tRNA(Ile) in addition to Val-tRNA(Ile), indicating that the valine-binding mode found in this study represents that in the Val-tRNA(Ile) editing reaction. Analyses of the Val-tRNA(Ile) editing activities of T. thermophilus IleRS mutants revealed the importance of Thr(228), Thr(229), Thr(230), and Asp(328), which are coordinated with water molecules in the present structure. The structural model for the Val-adenosine moiety of Val-tRNA(Ile) bound in the IleRS editing site revealed some interesting differences in the substrate binding and recognizing mechanisms between IleRS and T. thermophilus leucyl-tRNA synthetase. For example, the carbonyl oxygens of the amino acids are located opposite to each other, relative to the adenosine ribose ring, and are differently recognized.
-
-	Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.,Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S J Biol Chem. 2004 Feb 27;279(9):8396-402. Epub 2003 Dec 12. PMID:14672940<ref>PMID:14672940</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1udz" 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>

OCA at 09:54, 21 December 2022

OCA — Wed, 21 Dec 2022 09:54:52 GMT

←Older revision		Revision as of 09:54, 21 December 2022
Line 3:		Line 3:
	<StructureSection load='1udz' size='340' side='right'caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1udz' size='340' side='right'caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDZ 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;'>[[1ue0\|1ue0]]</div></td></tr>~~	+	</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [https://pdbe.org/1udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [https://www.ebi.ac.uk/pdbsum/1udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [https://www.topsan.org/Proteins/RSGI/1udz TOPSAN]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [https://pdbe.org/1udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [https://www.ebi.ac.uk/pdbsum/1udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [https://www.topsan.org/Proteins/RSGI/1udz 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]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: Isoleucine--tRNA ligase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukai, S]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Fukunaga, R]]	+	[[Category: Fukai S]]
-	[[Category: Ishitani, R]]	+	[[Category: Fukunaga R]]
-	[[Category: Nureki, O]]	+	[[Category: Ishitani R]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Nureki O]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Cp1]]~~	+
-	~~[[Category: Editing]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 09:41, 29 September 2021

OCA — Wed, 29 Sep 2021 09:41:13 GMT

←Older revision		Revision as of 09:41, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='1udz' size='340' side='right'caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1udz' size='340' side='right'caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ue0\|1ue0]]</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;'>[[1ue0\|1ue0]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [~~http~~://pdbe.org/1udz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1udz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1udz 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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [https://pdbe.org/1udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [https://www.ebi.ac.uk/pdbsum/1udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [https://www.topsan.org/Proteins/RSGI/1udz 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 06:08, 16 October 2019

OCA — Wed, 16 Oct 2019 06:08:35 GMT

←Older revision		Revision as of 06:08, 16 October 2019
Line 1:		Line 1:

	==Isoleucyl-tRNA synthetase editing domain==		==Isoleucyl-tRNA synthetase editing domain==
-	<StructureSection load='1udz' size='340' side='right' caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1udz' size='340' side='right'caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>
Line 32:		Line 32:

	==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 39:		Line 39:
	[[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: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]

OCA at 08:37, 21 March 2018

OCA — Wed, 21 Mar 2018 08:37:35 GMT

←Older revision		Revision as of 08:37, 21 March 2018
Line 1:		Line 1:
		+
	==Isoleucyl-tRNA synthetase editing domain==		==Isoleucyl-tRNA synthetase editing domain==
	<StructureSection load='1udz' size='340' side='right' caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1udz' size='340' side='right' caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://pdbe.org/1udz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://www.topsan.org/Proteins/RSGI/1udz 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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://pdbe.org/1udz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [http://www.topsan.org/Proteins/RSGI/1udz TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ud/1udz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ud/1udz_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 02:58, 10 February 2016

OCA — Wed, 10 Feb 2016 02:58:27 GMT

←Older revision		Revision as of 02:58, 10 February 2016
Line 18:		Line 18:
	<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=1udz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:42, 11 September 2015

OCA — Fri, 11 Sep 2015 04:42:32 GMT

←Older revision		Revision as of 04:42, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1udz' size='340' side='right' caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1udz' size='340' side='right' caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ue0\|1ue0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ue0\|1ue0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://www.topsan.org/Proteins/RSGI/1udz 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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://pdbe.org/1udz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://www.topsan.org/Proteins/RSGI/1udz TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1udz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]

OCA at 11:19, 25 December 2014

OCA — Thu, 25 Dec 2014 11:19:23 GMT

←Older revision		Revision as of 11:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ue0\|1ue0]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ue0\|1ue0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://www.topsan.org/Proteins/RSGI/1udz 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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://www.topsan.org/Proteins/RSGI/1udz 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 35:		Line 37:
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Fukai, S.]]	+	[[Category: Fukai, S]]
-	[[Category: Fukunaga, R.]]	+	[[Category: Fukunaga, R]]
-	[[Category: Ishitani, R.]]	+	[[Category: Ishitani, R]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Cp1]]		[[Category: Cp1]]
Line 47:		Line 49:
	[[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 04:13, 3 October 2014

OCA — Fri, 03 Oct 2014 04:13:02 GMT

←Older revision		Revision as of 04:13, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1udz~~\| ~~PDB~~=1udz \| ~~SCENE~~= }}	+	==Isoleucyl-tRNA synthetase editing domain==
-	===~~Isoleucyl~~-tRNA ~~synthetase editing domain~~===	+	<StructureSection load='1udz' size='340' side='right' caption='[[1udz]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_14672940}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ue0\|1ue0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">iles ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [http://www.ebi.ac.uk/pdbsum/1udz PDBsum], [http://www.topsan.org/Proteins/RSGI/1udz 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/ud/1udz_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 ==
		+	Isoleucyl-tRNA synthetase (IleRS) links tRNA(Ile) with not only its cognate isoleucine but also the nearly cognate valine. The CP1 domain of IleRS deacylates, or edits, the mischarged Val-tRNA(Ile). We determined the crystal structures of the Thermus thermophilus IleRS CP1 domain alone, and in its complex with valine at 1.8- and 2.0-A resolutions, respectively. In the complex structure, the Asp(328) residue, which was shown to be critical for the editing reaction against Val-tRNA(Ile) by a previous mutational analysis, recognizes the valine NH(3)(+) group. The valine side chain binding pocket is only large enough to accommodate valine, and the placement of an isoleucine model in this location revealed that the additional methylene group of isoleucine would clash with His(319). The H319A mutant of Escherichia coli IleRS reportedly deacylates the cognate Ile-tRNA(Ile) in addition to Val-tRNA(Ile), indicating that the valine-binding mode found in this study represents that in the Val-tRNA(Ile) editing reaction. Analyses of the Val-tRNA(Ile) editing activities of T. thermophilus IleRS mutants revealed the importance of Thr(228), Thr(229), Thr(230), and Asp(328), which are coordinated with water molecules in the present structure. The structural model for the Val-adenosine moiety of Val-tRNA(Ile) bound in the IleRS editing site revealed some interesting differences in the substrate binding and recognizing mechanisms between IleRS and T. thermophilus leucyl-tRNA synthetase. For example, the carbonyl oxygens of the amino acids are located opposite to each other, relative to the adenosine ribose ring, and are differently recognized.

-	~~==Function==~~	+	Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.,Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S J Biol Chem. 2004 Feb 27;279(9):8396-402. Epub 2003 Dec 12. PMID:14672940<ref>PMID:14672940</ref>
-	~~[[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]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1udz]] 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=1UDZ OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:014672940</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 02:48, 20 September 2013

OCA — Fri, 20 Sep 2013 02:48:56 GMT

←Older revision		Revision as of 02:48, 20 September 2013
Line 1:		Line 1:
-	[[Image:1udz.png\|left\|200px]]
-
	{{STRUCTURE_1udz\| PDB=1udz \| SCENE= }}		{{STRUCTURE_1udz\| PDB=1udz \| SCENE= }}
-
	===Isoleucyl-tRNA synthetase editing domain===		===Isoleucyl-tRNA synthetase editing domain===
		+	{{ABSTRACT_PUBMED_14672940}}

-	~~{{ABSTRACT_PUBMED_14672940}}~~	+	==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]

	==About this Structure==		==About this Structure==
Line 14:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:014672940</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014672940</ref><references group="xtra"/><references/>
	[[Category: Isoleucine--tRNA ligase]]		[[Category: Isoleucine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]