2e3c - Revision history

OCA at 08:34, 25 October 2023

OCA — Wed, 25 Oct 2023 08:34:19 GMT

←Older revision		Revision as of 08:34, 25 October 2023
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	<StructureSection load='2e3c' size='340' side='right'caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='2e3c' size='340' side='right'caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Dsm_2053 Dsm 2053~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E3C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E3C FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</div></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]] 2.65Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">pylS ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=2209 DSM 2053])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [https://pdbe.org/2e3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [https://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [https://www.topsan.org/Proteins/RSGI/2e3c 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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [https://pdbe.org/2e3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [https://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [https://www.topsan.org/Proteins/RSGI/2e3c TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).	+	[https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).
	== 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: Dsm 2053]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ishii, R~~]]	+	[[Category: Methanosarcina mazei]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Ishii R]]
-	[[Category: Yanagisawa, T]]	+	[[Category: Yanagisawa T]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Pyrrolysine]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Trna~~]]	+

OCA at 11:45, 10 February 2021

OCA — Wed, 10 Feb 2021 11:45:36 GMT

←Older revision		Revision as of 11:45, 10 February 2021
Line 1:		Line 1:

	==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase==		==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase==
-	<StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>	+	<StructureSection load='2e3c' size='340' side='right'caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E3C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E3C FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [~~http~~://pdbe.org/2e3c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2e3c 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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [https://pdbe.org/2e3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [https://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [https://www.topsan.org/Proteins/RSGI/2e3c TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).	+	[[https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl ~~tRNA Synthetase]]~~	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
-	*[[Pyrrolysyl-tRNA synthetase\|Pyrrolysyl-tRNA synthetase]]	+
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Dsm 2053]]		[[Category: Dsm 2053]]
		+	[[Category: Large Structures]]
	[[Category: Ishii, R]]		[[Category: Ishii, R]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 07:06, 6 June 2018

OCA — Wed, 06 Jun 2018 07:06:28 GMT

←Older revision		Revision as of 07:06, 6 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase==		==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase==
	<StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://pdbe.org/2e3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://www.topsan.org/Proteins/RSGI/2e3c 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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://pdbe.org/2e3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [http://www.topsan.org/Proteins/RSGI/2e3c 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/e3/2e3c_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e3/2e3c_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>
	</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=2e3c ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:27, 11 September 2015

OCA — Fri, 11 Sep 2015 09:27:27 GMT

←Older revision		Revision as of 09:27, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanosarcina_mazei Methanosarcina mazei~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E3C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E3C FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 ~~Methanosarcina mazei~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://www.topsan.org/Proteins/RSGI/2e3c 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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://pdbe.org/2e3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://www.topsan.org/Proteins/RSGI/2e3c 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 2e3c" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanosarcina mazei~~]]	+	[[Category: Dsm 2053]]
	[[Category: Ishii, R]]		[[Category: Ishii, R]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 14:30, 25 December 2014

OCA — Thu, 25 Dec 2014 14:30:10 GMT

←Older revision		Revision as of 14:30, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E3C FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E3C FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://www.topsan.org/Proteins/RSGI/2e3c 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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://www.topsan.org/Proteins/RSGI/2e3c TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
-	[[Category: Ishii, R.]]	+	[[Category: Ishii, R]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Yanagisawa, T.]]	+	[[Category: Yanagisawa, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Ligase]]		[[Category: Ligase]]
Line 44:		Line 46:
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	[[Category: Pyrrolysine]]		[[Category: Pyrrolysine]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Translation]]		[[Category: Translation]]
	[[Category: Trna]]		[[Category: Trna]]

OCA at 05:54, 29 September 2014

OCA — Mon, 29 Sep 2014 05:54:24 GMT

←Older revision		Revision as of 05:54, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2e3c.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase==
		+	<StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E3C FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dxg\|2dxg]], [[2dxh\|2dxh]], [[2dz8\|2dz8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://www.topsan.org/Proteins/RSGI/2e3c 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/e3/2e3c_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 ==
		+	Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the "22nd" genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA(Pyl) with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the "open" states to the "closed" states upon AMPPNP binding. On the other hand, the beta 7-beta 8 hairpin exhibits multiple conformational states, the open, intermediate (beta 7-open/beta 8-open and beta 7-closed/beta 8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the beta 7-beta 8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the beta 7-beta 8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA(Pyl). Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and alpha-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis.

-	~~{{STRUCTURE_2e3c\| PDB=2e3c \| SCENE= }}~~	+	Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.,Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S J Mol Biol. 2008 May 2;378(3):634-52. Epub 2008 Feb 29. PMID:18387634<ref>PMID:18387634</ref>

-	~~===Crystal structure~~ of the ~~catalytic domain of pyrrolysyl-tRNA synthetase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18387634}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2e3c]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanosarcina_mazei Methanosarcina mazei]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
	*[[Pyrrolysyl-tRNA synthetase\|Pyrrolysyl-tRNA synthetase]]		*[[Pyrrolysyl-tRNA synthetase\|Pyrrolysyl-tRNA synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018387634<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
	[[Category: Ishii, R.]]		[[Category: Ishii, R.]]

OCA at 17:50, 20 October 2012

OCA — Sat, 20 Oct 2012 17:50:30 GMT

←Older revision		Revision as of 17:50, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2e3c]] is a 1 chain structure ~~of [[Aminoacyl tRNA Synthetase]] and [[Pyrrolysyl-tRNA synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA].	+	[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA].

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

OCA: Protected "2e3c" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 02:10:11 GMT

Protected "2e3c" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:10, 27 July 2012

OCA at 02:10, 27 July 2012

OCA — Fri, 27 Jul 2012 02:10:09 GMT

←Older revision		Revision as of 02:10, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2e3c.png\|left\|200px]]		[[Image:2e3c.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2e3c", 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_2e3c\| PDB=2e3c \| SCENE= }}		{{STRUCTURE_2e3c\| PDB=2e3c \| SCENE= }}

	===Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase===		===Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18387634}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18387634 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18387634}}		{{ABSTRACT_PUBMED_18387634}}

	==About this Structure==		==About this Structure==
-	~~2E3C~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA].	+	[[2e3c]] is a 1 chain structure of [[Aminoacyl tRNA Synthetase]] and [[Pyrrolysyl-tRNA synthetase]] with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
		+	*[[Pyrrolysyl-tRNA synthetase\|Pyrrolysyl-tRNA synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18387634~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018387634</ref><references group="xtra"/>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
	[[Category: Ishii, R.]]		[[Category: Ishii, R.]]
Line 39:		Line 31:
	[[Category: Translation]]		[[Category: Translation]]
	[[Category: Trna]]		[[Category: Trna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:44:44 2009''

OCA at 16:44, 17 February 2009

OCA — Tue, 17 Feb 2009 16:44:46 GMT

←Older revision		Revision as of 16:44, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase., Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S, J Mol Biol. 2008 Feb 29;. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18387634 18387634]~~	+	<ref group="xtra">PMID:18387634</ref><references group="xtra"/>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
	[[Category: Ishii, R.]]		[[Category: Ishii, R.]]
Line 40:		Line 40:
	[[Category: Trna]]		[[Category: Trna]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16~~ 17:42:~~33 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:44:44 2009''