4ts1 - Revision history

OCA at 12:58, 1 March 2024

OCA — Fri, 01 Mar 2024 12:58:14 GMT

←Older revision		Revision as of 12:58, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='4ts1' size='340' side='right'caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ts1' size='340' side='right'caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=TYR:TYROSINE'>TYR</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]] 2.5Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [~~http~~://pdbe.org/4ts1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ts1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ts1 ProSAT]</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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [https://pdbe.org/4ts1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [https://www.ebi.ac.uk/pdbsum/4ts1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ts1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SYY_GEOSE SYY_GEOSE]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).	+	[https://www.uniprot.org/uniprot/SYY_GEOSE SYY_GEOSE] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=4ts1 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=4ts1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of a deletion mutant of tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been determined at 2.5 A resolution using molecular replacement techniques. The genetically engineered molecule catalyses the activation of tyrosine with kinetic properties similar to those of the wild-type enzyme but no longer binds tRNATyr. It contains 319 residues corresponding to the region of the polypeptide chain for which interpretable electron density is present in crystals of the wild-type enzyme. The partly refined model of the wild-type enzyme was used as a starting point in determining the structure of the truncated mutant. The new crystals are of space group P2(1) and contain the molecular dimer within the asymmetric unit. The refined model has a crystallographic R-factor of 18.7% for all reflections between 8 and 2.5 A. Each subunit contains two structural domains: the alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet and the alpha-helical domain (residues 248 to 319) containing five helices. The alpha/beta domains are related by a non-crystallographic dyad while the alpha-helical domains are in slightly different orientations in the two subunits. The tyrosine substrate binds in a slot at the bottom of a deep active site cleft in the middle of the alpha/beta domain. It is surrounded by polar side-chains and water molecules that are involved in an intricate hydrogen bonding network. Both the alpha-amino and hydroxyl groups of the substrate make good hydrogen bonds with the protein. The amino group forms hydrogen bonds with Tyr169-OH, Asp78-OD1 and Gln173-OE1. The phenolic hydroxyl group forms hydrogen bonds with Asp76-OD1 and Tyr34-OH. In contrast, the substrate carboxyl group makes no direct interactions with the enzyme. The results of both substrate inhibition studies and site-directed mutagenesis experiments have been examined in the light of the refined structure.
-
-	Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine.,Brick P, Blow DM J Mol Biol. 1987 Mar 20;194(2):287-97. PMID:3612807<ref>PMID:3612807</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ts1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]		*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Tyrosine--tRNA ligase]]~~	+	[[Category: Blow DM]]
-	[[Category: Blow~~, D M~~]]	+	[[Category: Brick P]]
-	[[Category: Brick, P]]	+

OCA at 14:31, 10 May 2019

OCA — Fri, 10 May 2019 14:31:20 GMT

←Older revision		Revision as of 14:31, 10 May 2019
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE==		==CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE==
-	<StructureSection load='4ts1' size='340' side='right' caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4ts1' size='340' side='right'caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://pdbe.org/4ts1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://pdbe.org/4ts1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ts1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ts/4ts1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ts/4ts1_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 30:		Line 31:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
		+	[[Category: Large Structures]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Blow, D M]]		[[Category: Blow, D M]]
	[[Category: Brick, P]]		[[Category: Brick, P]]

OCA at 23:28, 8 February 2016

OCA — Mon, 08 Feb 2016 23:28:35 GMT

←Older revision		Revision as of 23:28, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='4ts1' size='340' side='right' caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ts1' size='340' side='right' caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://pdbe.org/4ts1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~SYY_BACST SYY_BACST~~]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).~~[HAMAP-Rule:MF_02006]~~	+	[[http://www.uniprot.org/uniprot/SYY_GEOSE SYY_GEOSE]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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=4ts1 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 4ts1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geobacillus stearothermophilus~~]]	+	[[Category: Atcc 12980]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Blow, D M]]		[[Category: Blow, D M]]
	[[Category: Brick, P]]		[[Category: Brick, P]]

OCA at 02:52, 25 December 2014

OCA — Thu, 25 Dec 2014 02:52:59 GMT

←Older revision		Revision as of 02:52, 25 December 2014
Line 7:		Line 7:
	<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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYY_BACST SYY_BACST]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).[HAMAP-Rule:MF_02006]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 17:02, 10 December 2014

OCA — Wed, 10 Dec 2014 17:02:44 GMT

←Older revision		Revision as of 17:02, 10 December 2014
Line 1:		Line 1:
-	[[~~Image~~:4ts1.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE==
		+	<StructureSection load='4ts1' size='340' side='right' caption='[[4ts1]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ts1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TS1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=4ts1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ts1 RCSB], [http://www.ebi.ac.uk/pdbsum/4ts1 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/ts/4ts1_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 ==
		+	The crystal structure of a deletion mutant of tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been determined at 2.5 A resolution using molecular replacement techniques. The genetically engineered molecule catalyses the activation of tyrosine with kinetic properties similar to those of the wild-type enzyme but no longer binds tRNATyr. It contains 319 residues corresponding to the region of the polypeptide chain for which interpretable electron density is present in crystals of the wild-type enzyme. The partly refined model of the wild-type enzyme was used as a starting point in determining the structure of the truncated mutant. The new crystals are of space group P2(1) and contain the molecular dimer within the asymmetric unit. The refined model has a crystallographic R-factor of 18.7% for all reflections between 8 and 2.5 A. Each subunit contains two structural domains: the alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet and the alpha-helical domain (residues 248 to 319) containing five helices. The alpha/beta domains are related by a non-crystallographic dyad while the alpha-helical domains are in slightly different orientations in the two subunits. The tyrosine substrate binds in a slot at the bottom of a deep active site cleft in the middle of the alpha/beta domain. It is surrounded by polar side-chains and water molecules that are involved in an intricate hydrogen bonding network. Both the alpha-amino and hydroxyl groups of the substrate make good hydrogen bonds with the protein. The amino group forms hydrogen bonds with Tyr169-OH, Asp78-OD1 and Gln173-OE1. The phenolic hydroxyl group forms hydrogen bonds with Asp76-OD1 and Tyr34-OH. In contrast, the substrate carboxyl group makes no direct interactions with the enzyme. The results of both substrate inhibition studies and site-directed mutagenesis experiments have been examined in the light of the refined structure.

-	~~{{STRUCTURE_4ts1\| PDB=4ts1 \| SCENE= }}~~	+	Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine.,Brick P, Blow DM J Mol Biol. 1987 Mar 20;194(2):287-97. PMID:3612807<ref>PMID:3612807</ref>

-	~~===CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T~~/~~RNA SYNTHETASE COMPLEXED WITH TYROSINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_3612807}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[4ts1]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:003612807<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
-	[[Category: Blow, D M.]]	+	[[Category: Blow, D M]]
-	[[Category: Brick, P.]]	+	[[Category: Brick, P]]

OCA at 11:50, 20 October 2012

OCA — Sat, 20 Oct 2012 11:50:15 GMT

←Older revision		Revision as of 11:50, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[4ts1]] is a 2 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].	+	[[4ts1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:003612807~~</ref><ref group="xtra">PMID:012215419~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:003612807</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Blow, D M.]]		[[Category: Blow, D M.]]
	[[Category: Brick, P.]]		[[Category: Brick, P.]]

OCA: Protected "4ts1" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 06:45:40 GMT

Protected "4ts1" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:45, 26 July 2012

OCA at 06:45, 26 July 2012

OCA — Thu, 26 Jul 2012 06:45:39 GMT

←Older revision		Revision as of 06:45, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:4ts1.png\|left\|200px]]		[[Image:4ts1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_4ts1", 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_4ts1\| PDB=4ts1 \| SCENE= }}		{{STRUCTURE_4ts1\| PDB=4ts1 \| SCENE= }}

	===CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE===		===CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_3612807}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 3612807 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_3612807}}		{{ABSTRACT_PUBMED_3612807}}

	==About this Structure==		==About this Structure==
-	~~4TS1~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].	+	[[4ts1]] is a 2 chain structure of [[Aminoacyl tRNA Synthetase]] with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~3612807~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:003612807</ref><ref group="xtra">PMID:012215419</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Blow, D M.]]		[[Category: Blow, D M.]]
	[[Category: Brick, P.]]		[[Category: Brick, P.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:24:06 2009''

OCA at 02:24, 17 February 2009

OCA — Tue, 17 Feb 2009 02:24:06 GMT

←Older revision		Revision as of 02:24, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	4TS1 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].	+	4TS1 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS1 OCA].

	==Reference==		==Reference==
-	~~Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine., Brick P, Blow DM, J Mol Biol. 1987 Mar 20;194(2):287-97.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/3612807 3612807]~~	+	<ref group="xtra">PMID:3612807</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Single protein]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Blow, D M.]]		[[Category: Blow, D M.]]
	[[Category: Brick, P.]]		[[Category: Brick, P.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 13~~:53:~~18 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:24:06 2009''

OCA at 10:53, 3 July 2008

OCA — Thu, 03 Jul 2008 10:53:18 GMT

←Older revision		Revision as of 10:53, 3 July 2008
Line 1:		Line 1:
-	[[Image:4ts1.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:4ts1.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_4ts1\| PDB=4ts1 \| SCENE= }}		{{STRUCTURE_4ts1\| PDB=4ts1 \| SCENE= }}

-	~~'''~~CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE~~'''~~	+	===CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE===


-	~~==Overview==~~	+	<!--
-	The crystal structure of a deletion mutant of tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been determined at 2.5 A resolution using molecular replacement techniques. The genetically engineered molecule catalyses the ~~activation of tyrosine with kinetic properties similar~~ to ~~those of~~ the wild-type enzyme but no longer binds tRNATyr. It contains 319 residues corresponding to the region of the polypeptide chain for which interpretable electron density is present in crystals of the wild-type enzyme. The partly refined model of the wild-type enzyme was used as a starting point in determining the structure of the truncated mutant. The new crystals are of space group P2(1) and contain the molecular dimer within the asymmetric unit. The refined model has a crystallographic R-factor of 18.7% for all reflections between 8 and 2.5 A. Each subunit contains two structural domains: ~~the alpha~~/~~beta domain (residues 1 to 220) containing a six-stranded beta-sheet and the alpha-helical domain (residues 248 to 319) containing five helices. The alpha~~/~~beta domains are related by a non-crystallographic dyad while the alpha-helical domains are in slightly different orientations in the two subunits~~. ~~The tyrosine substrate binds in a slot at the bottom of a deep active site cleft in the middle of the alpha/beta domain~~. It is ~~surrounded by polar side-chains and water molecules that are involved in an intricate hydrogen bonding network. Both~~ the ~~alpha-amino and hydroxyl groups of the substrate make good hydrogen bonds with the protein~~. ~~The amino group forms hydrogen bonds with Tyr169~~-~~OH, Asp78~~-OD1 and Gln173-OE1. The phenolic hydroxyl group forms hydrogen bonds with Asp76-OD1 and Tyr34-OH. In contrast, the substrate carboxyl group makes no direct interactions with the enzyme. The results of both substrate inhibition studies and site-directed mutagenesis experiments have been examined in the light of the refined structure.	+	The line below this paragraph, {{ABSTRACT_PUBMED_3612807}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 3612807 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_3612807}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Blow, D M.]]		[[Category: Blow, D M.]]
	[[Category: Brick, P.]]		[[Category: Brick, P.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:30:37 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:53:18 2008''