1gax - Revision history

OCA at 23:29, 27 December 2023

OCA — Wed, 27 Dec 2023 23:29:12 GMT

←Older revision		Revision as of 23:29, 27 December 2023
Line 3:		Line 3:
	<StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GAX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GAX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=VAA:N~~-[~~VALINYL]-N-~~[~~ADENOSYL~~]~~-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;'>~~[~~[1ile\|1ile~~]], [~~[1qu2\|1qu2~~]~~]</div~~></td><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [https://pdbe.org/1gax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [https://www.ebi.ac.uk/pdbsum/1gax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gax ProSAT], [https://www.topsan.org/Proteins/RSGI/1gax 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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [https://pdbe.org/1gax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [https://www.ebi.ac.uk/pdbsum/1gax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gax ProSAT], [https://www.topsan.org/Proteins/RSGI/1gax TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]	+	[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: ~~Valine--tRNA ligase~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Fukai, S]]	+	[[Category: Fukai S]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sekine S]]
-	[[Category: Sekine, S]]	+	[[Category: Shimada A]]
-	[[Category: Shimada, A]]	+	[[Category: Tao J]]
-	[[Category: Tao, J]]	+	[[Category: Vassylyev DG]]
-	[[Category: Vassylyev~~, D G~~]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Coiled coil]]~~	+
-	~~[[Category: Ligase-rna complex]]~~	+
-	~~[[Category: Protein-rna complex]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Trna~~]]	+

OCA at 11:20, 28 July 2021

OCA — Wed, 28 Jul 2021 11:20:43 GMT

←Older revision		Revision as of 11:20, 28 July 2021
Line 3:		Line 3:
	<StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1GAX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GAX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ile\|1ile]], [[1qu2\|1qu2]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [~~http~~://pdbe.org/1gax PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gax PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gax ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1gax 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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [https://pdbe.org/1gax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [https://www.ebi.ac.uk/pdbsum/1gax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gax ProSAT], [https://www.topsan.org/Proteins/RSGI/1gax TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]	+	[[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:37, 23 October 2019

OCA — Wed, 23 Oct 2019 08:37:02 GMT

←Older revision		Revision as of 08:37, 23 October 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==		==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==
-	<StructureSection load='1gax' size='340' side='right' caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[~~TRNA~~\|~~TRNA~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
		+	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 40:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]

OCA at 06:23, 3 January 2018

OCA — Wed, 03 Jan 2018 06:23:18 GMT

←Older revision		Revision as of 06:23, 3 January 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==		==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==
	<StructureSection load='1gax' size='340' side='right' caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1gax' size='340' side='right' caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://pdbe.org/1gax PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax 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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://pdbe.org/1gax PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gax ProSAT], [http://www.topsan.org/Proteins/RSGI/1gax 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/ga/1gax_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/1gax_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 31:		Line 32:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
	*[[TRNA\|TRNA]]		*[[TRNA\|TRNA]]
	== References ==		== References ==
Line 49:		Line 49:
	[[Category: Vassylyev, D G]]		[[Category: Vassylyev, D G]]
	[[Category: Yokoyama, S]]		[[Category: Yokoyama, S]]
		+	[[Category: Coiled coil]]
	[[Category: Ligase-rna complex]]		[[Category: Ligase-rna complex]]
	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]

OCA at 12:49, 8 February 2016

OCA — Mon, 08 Feb 2016 12:49:51 GMT

←Older revision		Revision as of 12:49, 8 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=1gax ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:44, 10 September 2015

OCA — Thu, 10 Sep 2015 11:44:37 GMT

←Older revision		Revision as of 11:44, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1gax' size='340' side='right' caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1gax' size='340' side='right' caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax 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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://pdbe.org/1gax PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax 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 1gax" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Thermus thermophilus]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]

OCA at 23:25, 24 December 2014

OCA — Wed, 24 Dec 2014 23:25:31 GMT

←Older revision		Revision as of 23:25, 24 December 2014
Line 8:		Line 8:
	<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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax 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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYV_THETH SYV_THETH]] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 20:15, 22 December 2014

OCA — Mon, 22 Dec 2014 20:15:50 GMT

←Older revision		Revision as of 20:15, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax 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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 38:
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Valine--tRNA ligase]]		[[Category: Valine--tRNA ligase]]
-	[[Category: Fukai, S.]]	+	[[Category: Fukai, S]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Shimada, A.]]	+	[[Category: Shimada, A]]
-	[[Category: Tao, J.]]	+	[[Category: Tao, J]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Ligase-rna complex]]		[[Category: Ligase-rna complex]]
	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Trna]]		[[Category: Trna]]

OCA at 14:59, 29 September 2014

OCA — Mon, 29 Sep 2014 14:59:18 GMT

←Older revision		Revision as of 14:59, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1gax\| PDB=1gax \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==
-	===CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE===	+	<StructureSection load='1gax' size='340' side='right' caption='[[1gax]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_11114335}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GAX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ile\|1ile]], [[1qu2\|1qu2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.topsan.org/Proteins/RSGI/1gax 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/ga/1gax_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 ==
		+	Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.

-	~~==About this Structure==~~	+	Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.,Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S Cell. 2000 Nov 22;103(5):793-803. PMID:11114335<ref>PMID:11114335</ref>
-	~~[[1gax]] is a 4 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule~~ of ~~the Month] feature on ''Aminoacyl~~-tRNA ~~Synthetases'' by David~~ S. ~~Goodsell is [http~~:~~//dx~~.~~doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1GAX OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
	*[[TRNA\|TRNA]]		*[[TRNA\|TRNA]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011114335<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]

OCA at 10:19, 11 March 2013

OCA — Mon, 11 Mar 2013 10:19:43 GMT

←Older revision		Revision as of 10:19, 11 March 2013
Line 1:		Line 1:
-	[[Image:1gax.png\|left\|200px]]
-
	{{STRUCTURE_1gax\| PDB=1gax \| SCENE= }}		{{STRUCTURE_1gax\| PDB=1gax \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE===		===CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE===
-
	{{ABSTRACT_PUBMED_11114335}}		{{ABSTRACT_PUBMED_11114335}}