1j09 - Revision history

OCA at 07:13, 25 October 2023

2023-10-25T07:13:40Z

←Older revision		Revision as of 07:13, 25 October 2023
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	<StructureSection load='1j09' size='340' side='right'caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1j09' size='340' side='right'caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J09 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J09 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17]~~ </~~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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [https://pdbe.org/1j09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [https://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j09 ProSAT], [https://www.topsan.org/Proteins/RSGI/1j09 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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [https://pdbe.org/1j09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [https://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j09 ProSAT], [https://www.topsan.org/Proteins/RSGI/1j09 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8]] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref>	+	[https://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref>
	== 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: Glutamate--tRNA ligase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernier, S]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Chenevert, R]]	+	[[Category: Bernier S]]
-	[[Category: Dubois~~, D Y~~]]	+	[[Category: Chenevert R]]
-	[[Category: Lapointe, J]]	+	[[Category: Dubois DY]]
-	[[Category: Nureki, O]]	+	[[Category: Lapointe J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Nureki O]]
-	[[Category: Sekine, S]]	+	[[Category: Sekine S]]
-	[[Category: Vassylyev~~, D G~~]]	+	[[Category: Vassylyev DG]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Glurs-atp-glu complex]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 11:08, 4 August 2021

2021-08-04T11:08:42Z

←Older revision		Revision as of 11:08, 4 August 2021
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	<StructureSection load='1j09' size='340' side='right'caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1j09' size='340' side='right'caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1J09 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J09 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [~~http~~://pdbe.org/1j09 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1j09 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1j09 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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [https://pdbe.org/1j09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [https://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j09 ProSAT], [https://www.topsan.org/Proteins/RSGI/1j09 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8]] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref>	+	[[https://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8]] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:13, 30 October 2019

2019-10-30T10:13:31Z

←Older revision		Revision as of 10:13, 30 October 2019
Line 1:		Line 1:

	==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu==		==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu==
-	<StructureSection load='1j09' size='340' side='right' caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1j09' size='340' side='right'caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1j09" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1j09" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Glutamate--tRNA ligase]]		[[Category: Glutamate--tRNA ligase]]
		+	[[Category: Large Structures]]
	[[Category: Bernier, S]]		[[Category: Bernier, S]]
	[[Category: Chenevert, R]]		[[Category: Chenevert, R]]

OCA at 08:58, 17 January 2018

2018-01-17T08:58:57Z

←Older revision		Revision as of 08:58, 17 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu==		==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu==
	<StructureSection load='1j09' size='340' side='right' caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1j09' size='340' side='right' caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://pdbe.org/1j09 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://www.topsan.org/Proteins/RSGI/1j09 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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://pdbe.org/1j09 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j09 ProSAT], [http://www.topsan.org/Proteins/RSGI/1j09 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/j0/1j09_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j0/1j09_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1j09" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1j09" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:39, 9 February 2016

2016-02-09T11:39:28Z

←Older revision		Revision as of 11:39, 9 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=1j09 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:51, 10 September 2015

2015-09-10T21:51:03Z

←Older revision		Revision as of 21:51, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1j09' size='340' side='right' caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1j09' size='340' side='right' caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://www.topsan.org/Proteins/RSGI/1j09 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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://pdbe.org/1j09 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://www.topsan.org/Proteins/RSGI/1j09 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 1j09" 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: Glutamate--tRNA ligase]]		[[Category: Glutamate--tRNA ligase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Bernier, S]]		[[Category: Bernier, S]]
	[[Category: Chenevert, R]]		[[Category: Chenevert, R]]

OCA at 06:33, 25 December 2014

2014-12-25T06:33:23Z

←Older revision		Revision as of 06:33, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://www.topsan.org/Proteins/RSGI/1j09 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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://www.topsan.org/Proteins/RSGI/1j09 TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8]] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Glutamate--tRNA ligase]]		[[Category: Glutamate--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Bernier, S.]]	+	[[Category: Bernier, S]]
-	[[Category: Chenevert, R.]]	+	[[Category: Chenevert, R]]
-	[[Category: Dubois, D Y.]]	+	[[Category: Dubois, D Y]]
-	[[Category: Lapointe, J.]]	+	[[Category: Lapointe, J]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Glurs-atp-glu complex]]		[[Category: Glurs-atp-glu complex]]
	[[Category: Ligase]]		[[Category: Ligase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 14:15, 28 September 2014

2014-09-28T14:15:33Z

←Older revision		Revision as of 14:15, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1j09.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu==
		+	<StructureSection load='1j09' size='340' side='right' caption='[[1j09]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1j09]] 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=1J09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J09 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g59\|1g59]], [[1gln\|1gln]], [[1n75\|1n75]], [[1n77\|1n77]], [[1n78\|1n78]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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=1j09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j09 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j09 RCSB], [http://www.ebi.ac.uk/pdbsum/1j09 PDBsum], [http://www.topsan.org/Proteins/RSGI/1j09 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/j0/1j09_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 ==
		+	Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.

-	~~{{STRUCTURE_1j09\| PDB=1j09 \| SCENE= }}~~	+	ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.,Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668<ref>PMID:12554668</ref>

-	~~===Crystal structure~~ of ~~Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12554668}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1j09]] 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=1J09 OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012554668<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Glutamate--tRNA ligase]]		[[Category: Glutamate--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 13:43, 20 October 2012

2012-10-20T13:43:11Z

←Older revision		Revision as of 13:43, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1j09]] 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=1J09 OCA].	+	[[1j09]] 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=1J09 OCA].

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

OCA: Protected "1j09" [edit=sysop:move=sysop]

2012-07-26T12:52:55Z

Protected "1j09" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:52, 26 July 2012