1vbm - Revision history

OCA at 07:51, 25 October 2023

2023-10-25T07:51:33Z

←Older revision		Revision as of 07:51, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1vbm' size='340' side='right'caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1vbm' size='340' side='right'caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBM FirstGlance]. <br>
-	</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=YSA:5-O-~~[~~N-(L-TYROSYL)SULFAMOYL~~]~~ADENOSINE'>YSA</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]~~</~~div~~><~~/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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tyrosine~~--~~tRNA_ligase Tyrosine~~--~~tRNA ligase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [https://pdbe.org/1vbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [https://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbm ProSAT], [https://www.topsan.org/Proteins/RSGI/1vbm 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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [https://pdbe.org/1vbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [https://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbm ProSAT], [https://www.topsan.org/Proteins/RSGI/1vbm TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI]] 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]	+	[https://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI] 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]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Tyrosine--tRNA ligase]]~~	+	[[Category: Kamata K]]
-	[[Category: Kamata, K]]	+	[[Category: Kobayashi T]]
-	[[Category: Kobayashi, T]]	+	[[Category: Nishimura S]]
-	[[Category: Nishimura, S]]	+	[[Category: Sakamoto K]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sekine R]]
-	[[Category: Sakamoto, K]]	+	[[Category: Takimura T]]
-	[[Category: Sekine, R]]	+	[[Category: Yokoyama S]]
-	[[Category: Takimura, T]]	+
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 13:19, 13 October 2021

2021-10-13T13:19:38Z

←Older revision		Revision as of 13:19, 13 October 2021
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	<StructureSection load='1vbm' size='340' side='right'caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1vbm' size='340' side='right'caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1VBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBM 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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>	+	</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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</div></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'>[https://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [https://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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [~~http~~://pdbe.org/1vbm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbm ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1vbm 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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [https://pdbe.org/1vbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [https://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbm ProSAT], [https://www.topsan.org/Proteins/RSGI/1vbm TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI]] 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]	+	[[https://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI]] 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 10:38, 8 January 2020

2020-01-08T10:38:54Z

←Older revision		Revision as of 10:38, 8 January 2020
Line 1:		Line 1:

	==Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS==		==Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS==
-	<StructureSection load='1vbm' size='340' side='right' caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1vbm' size='340' side='right'caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM FirstGlance]. <br>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Kamata, K]]		[[Category: Kamata, K]]

OCA at 07:43, 4 April 2018

2018-04-04T07:43:06Z

←Older revision		Revision as of 07:43, 4 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS==		==Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS==
	<StructureSection load='1vbm' size='340' side='right' caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1vbm' size='340' side='right' caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://pdbe.org/1vbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbm 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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://pdbe.org/1vbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbm ProSAT], [http://www.topsan.org/Proteins/RSGI/1vbm TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vb/1vbm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vb/1vbm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:10, 8 February 2016

2016-02-08T03:10:01Z

←Older revision		Revision as of 03:10, 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=1vbm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:18, 10 September 2015

2015-09-10T07:18:12Z

←Older revision		Revision as of 07:18, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1vbm' size='340' side='right' caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1vbm' size='340' side='right' caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM 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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbm 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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://pdbe.org/1vbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbm 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 1vbm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Kamata, K]]		[[Category: Kamata, K]]

OCA at 20:08, 24 December 2014

2014-12-24T20:08:45Z

←Older revision		Revision as of 20:08, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM 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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbm 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=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbm TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI]] 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]]
Line 35:		Line 37:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
-	[[Category: Kamata, K.]]	+	[[Category: Kamata, K]]
-	[[Category: Kobayashi, T.]]	+	[[Category: Kobayashi, T]]
-	[[Category: Nishimura, S.]]	+	[[Category: Nishimura, S]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sakamoto, K.]]	+	[[Category: Sakamoto, K]]
-	[[Category: Sekine, R.]]	+	[[Category: Sekine, R]]
-	[[Category: Takimura, T.]]	+	[[Category: Takimura, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Ligase]]		[[Category: Ligase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 22:32, 28 September 2014

2014-09-28T22:32:24Z

←Older revision		Revision as of 22:32, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1vbm.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS==
		+	<StructureSection load='1vbm' size='340' side='right' caption='[[1vbm]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBM 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=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1udf\|1udf]], [[1udj\|1udj]], [[1vbn\|1vbn]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vbm RCSB], [http://www.ebi.ac.uk/pdbsum/1vbm PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbm 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/vb/1vbm_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 ==
		+	Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.

-	~~{{STRUCTURE_1vbm\| PDB=1vbm \| SCENE= }}~~	+	Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.,Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S J Mol Biol. 2005 Feb 11;346(1):105-17. Epub 2004 Dec 15. PMID:15663931<ref>PMID:15663931</ref>

-	~~===Crystal structure~~ of the ~~Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15663931}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1vbm]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015663931<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]

OCA at 08:42, 20 October 2012

2012-10-20T08:42:38Z

←Older revision		Revision as of 08:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1vbm]] is a 2 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA].	+	[[1vbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBM OCA].

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

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

2012-07-25T20:30:35Z

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

←Older revision

Revision as of 20:30, 25 July 2012