3kt6 - Revision history

OCA at 16:17, 1 November 2023

OCA — Wed, 01 Nov 2023 16:17:51 GMT

←Older revision		Revision as of 16:17, 1 November 2023
Line 1:		Line 1:

	==Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp==		==Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp==
-	<StructureSection load='3kt6' size='340' side='right' caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='3kt6' size='340' side='right'caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 2.8Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kt0\|3kt0]]~~, [[~~3kt3~~\|~~3kt3]], [[3kt8\|3kt8~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4932 ATCC 18824])</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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [https://pdbe.org/3kt6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [https://www.ebi.ac.uk/pdbsum/3kt6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kt6 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2]~~ </~~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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [~~http~~://pdbe.org/3kt6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kt6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kt6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYWC_YEAST SYWC_YEAST]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kt/3kt6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kt/3kt6_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 29:
	</div>		</div>
	<div class="pdbe-citations 3kt6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3kt6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 18824~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Tryptophan--tRNA ligase~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Ding, J]]	+	[[Category: Ding J]]
-	[[Category: Dong, X]]	+	[[Category: Dong X]]
-	[[Category: Shen, N]]	+	[[Category: Shen N]]
-	[[Category: Zhong, C]]	+	[[Category: Zhong C]]
-	[[Category: Zhou, M]]	+	[[Category: Zhou M]]
-	~~[[Category: Amino acid activation]]~~	+
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Catalytic mechanism]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Protein biosynthesis]]~~	+
-	~~[[Category: S. cerevisiae]]~~	+
-	~~[[Category: Sulfate ion]]~~	+
-	~~[[Category: Tryptophanyl-trna synthetase~~]]	+

OCA at 08:41, 1 November 2017

OCA — Wed, 01 Nov 2017 08:41:01 GMT

←Older revision		Revision as of 08:41, 1 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp==		==Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp==
	<StructureSection load='3kt6' size='340' side='right' caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3kt6' size='340' side='right' caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://pdbe.org/3kt6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum]</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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://pdbe.org/3kt6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kt6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3kt6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3kt6" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
	== References ==		== References ==
	<references/>		<references/>
Line 46:		Line 44:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
		+	[[Category: Cytoplasm]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]

OCA at 23:58, 8 February 2016

OCA — Mon, 08 Feb 2016 23:58:11 GMT

←Older revision		Revision as of 23:58, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3kt6' size='340' side='right' caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3kt6' size='340' side='right' caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kt0\|3kt0]], [[3kt3\|3kt3]], [[3kt8\|3kt8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kt0\|3kt0]], [[3kt3\|3kt3]], [[3kt8\|3kt8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum]</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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://pdbe.org/3kt6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 17:
	<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=3kt6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3kt6" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Tryptophan--tRNA ligase]]		[[Category: Tryptophan--tRNA ligase]]
	[[Category: Ding, J]]		[[Category: Ding, J]]

OCA at 08:29, 20 January 2015

OCA — Tue, 20 Jan 2015 08:29:37 GMT

←Older revision		Revision as of 08:29, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kt0\|3kt0]], [[3kt3\|3kt3]], [[3kt8\|3kt8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kt0\|3kt0]], [[3kt3\|3kt3]], [[3kt8\|3kt8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum]</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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Tryptophan--tRNA ligase]]		[[Category: Tryptophan--tRNA ligase]]
-	[[Category: Ding, J.]]	+	[[Category: Ding, J]]
-	[[Category: Dong, X.]]	+	[[Category: Dong, X]]
-	[[Category: Shen, N.]]	+	[[Category: Shen, N]]
-	[[Category: Zhong, C.]]	+	[[Category: Zhong, C]]
-	[[Category: Zhou, M.]]	+	[[Category: Zhou, M]]
	[[Category: Amino acid activation]]		[[Category: Amino acid activation]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]

OCA at 11:15, 29 September 2014

OCA — Mon, 29 Sep 2014 11:15:14 GMT

←Older revision		Revision as of 11:15, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3kt6.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp==
		+	<StructureSection load='3kt6' size='340' side='right' caption='[[3kt6]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kt6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KT6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kt0\|3kt0]], [[3kt3\|3kt3]], [[3kt8\|3kt8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </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=3kt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kt6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kt6 PDBsum]</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/kt/3kt6_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 ==
		+	Specific activation of amino acids by aminoacyl-tRNA synthetases is essential for maintaining translational fidelity. Here, we present crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase (sTrpRS) in apo form and in complexes with various ligands. In each complex, there is a sulfate ion bound at the active site which mimics the alpha- or beta-phosphate group of ATP during tryptophan activation. In particular, in one monomer of the sTrpRS-TrpNH(2)O complex, the sulfate ion appears to capture a snapshot of the alpha-phosphate of ATP during its movement towards tryptophan. Simulation study of a human TrpRS-Trp-ATP model shows that during the catalytic process the alpha-phosphate of ATP is driven to an intermediate position equivalent to that of the sulfate ion, then moves further and eventually fluctuates at around 2 A from the nucleophile. A conserved Arg may interact with the oxygen in the scissile bond at the transition state, indicating its critical role in the nucleophilic substitution. Taken together, eukaryotic TrpRSs may adopt an associative mechanism for tryptophan activation in contrast to a dissociative mechanism proposed for bacterial TrpRSs. In addition, structural analysis of the apo sTrpRS reveals a unique feature of fungal TrpRSs, which could be exploited in rational antifungal drug design.

-	~~{{STRUCTURE_3kt6\| PDB=3kt6 \| SCENE= }}~~	+	Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design.,Zhou M, Dong X, Shen N, Zhong C, Ding J Nucleic Acids Res. 2010 Jun;38(10):3399-413. Epub 2010 Jan 31. PMID:20123733<ref>PMID:20123733</ref>

-	~~===Crystal structure~~ of S. ~~cerevisiae tryptophanyl-tRNA synthetase in complex with Trp===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20123733}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3kt6]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020123733<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Tryptophan--tRNA ligase]]		[[Category: Tryptophan--tRNA ligase]]

OCA at 11:55, 20 October 2012

OCA — Sat, 20 Oct 2012 11:55:11 GMT

←Older revision		Revision as of 11:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3kt6]] is a 4 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA].	+	[[3kt6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA].

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

OCA: Protected "3kt6" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 07:01:34 GMT

Protected "3kt6" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:01, 26 July 2012

OCA at 07:01, 26 July 2012

OCA — Thu, 26 Jul 2012 07:01:33 GMT

←Older revision		Revision as of 07:01, 26 July 2012
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-	{{Seed}}
	[[Image:3kt6.png\|left\|200px]]		[[Image:3kt6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kt6", 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_3kt6\| PDB=3kt6 \| SCENE= }}		{{STRUCTURE_3kt6\| PDB=3kt6 \| SCENE= }}

	===Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp===		===Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20123733}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20123733 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_20123733}}		{{ABSTRACT_PUBMED_20123733}}

	==About this Structure==		==About this Structure==
-	~~3KT6~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA].	+	[[3kt6]] is a 4 chain structure of [[Aminoacyl tRNA Synthetase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20123733~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020123733</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Tryptophan--tRNA ligase]]		[[Category: Tryptophan--tRNA ligase]]
Line 35:		Line 26:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
-	[[Category: Cytoplasm]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
Line 42:		Line 32:
	[[Category: Sulfate ion]]		[[Category: Sulfate ion]]
	[[Category: Tryptophanyl-trna synthetase]]		[[Category: Tryptophanyl-trna synthetase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:25:23 2010''

OCA at 04:20, 16 June 2010

OCA — Wed, 16 Jun 2010 04:20:22 GMT

←Older revision		Revision as of 04:20, 16 June 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3kt6.~~jpg~~\|left\|200px]]	+	[[Image:3kt6.png\|left\|200px]]

	<!--		<!--
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	[[Category: Tryptophanyl-trna synthetase]]		[[Category: Tryptophanyl-trna synthetase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 17 10~~:38:10 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:25:23 2010''

OCA at 08:38, 17 February 2010

OCA — Wed, 17 Feb 2010 08:38:10 GMT

←Older revision		Revision as of 08:38, 17 February 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kt6.jpg\|left\|200px]]

-	The ~~entry 3kt6~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kt6", 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_3kt6\| PDB=3kt6 \| SCENE= }}

-	~~Authors: Zhou, M., Dong, X., Zhong, C., Shen, N., Ding, J~~.	+	===Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp===

-	Description: Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 9 14~~:44:~~26 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20123733}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20123733 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20123733}}
		+
		+	==About this Structure==
		+	3KT6 is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KT6 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20123733</ref><references group="xtra"/>
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Tryptophan--tRNA ligase]]
		+	[[Category: Ding, J.]]
		+	[[Category: Dong, X.]]
		+	[[Category: Shen, N.]]
		+	[[Category: Zhong, C.]]
		+	[[Category: Zhou, M.]]
		+	[[Category: Amino acid activation]]
		+	[[Category: Aminoacyl-trna synthetase]]
		+	[[Category: Atp-binding]]
		+	[[Category: Catalytic mechanism]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Ligase]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Protein biosynthesis]]
		+	[[Category: S. cerevisiae]]
		+	[[Category: Sulfate ion]]
		+	[[Category: Tryptophanyl-trna synthetase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 17 10:38:10 2010''