2zio - Revision history

OCA at 13:36, 1 November 2023

OCA — Wed, 01 Nov 2023 13:36:54 GMT

←Older revision		Revision as of 13:36, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zio' size='340' side='right'caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2zio' size='340' side='right'caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>~~, ~~<scene name='pdbligand=AYB:5-O-~~[~~(S)-({(2S)-2-AMINO-6-~~[~~(PROPOXYCARBONYL)AMINO~~]~~HEXANOYL}OXY)(HYDROXY)PHOSPHORYL~~]~~ADENOSINE'>AYB</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]] 2.06Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [https://pdbe.org/2zio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [https://www.ebi.ac.uk/pdbsum/2zio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zio ProSAT], [https://www.topsan.org/Proteins/RSGI/2zio 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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [https://pdbe.org/2zio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [https://www.ebi.ac.uk/pdbsum/2zio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zio ProSAT], [https://www.topsan.org/Proteins/RSGI/2zio 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: Atp analogue]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Non-natural amino acid]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Protein biosynthesis]]~~	+
-	~~[[Category: Pyrrolysine]]~~	+
-	~~[[Category: Pyrrolysyl-trna synthetase]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Trna]]~~	+
-	~~[[Category: Unnatural amino acid~~]]	+

OCA at 17:30, 15 December 2021

OCA — Wed, 15 Dec 2021 17:30:51 GMT

←Older revision		Revision as of 17:30, 15 December 2021
Line 1:		Line 1:

	==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP==		==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP==
-	<StructureSection load='2zio' size='340' side='right' caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>	+	<StructureSection load='2zio' size='340' side='right'caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [~~http~~://pdbe.org/2zio PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zio PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zio ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2zio 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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [https://pdbe.org/2zio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [https://www.ebi.ac.uk/pdbsum/2zio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zio ProSAT], [https://www.topsan.org/Proteins/RSGI/2zio 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 33:		Line 33:

	==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 39:		Line 39:
	</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 07:20, 18 October 2018

OCA — Thu, 18 Oct 2018 07:20:03 GMT

←Older revision		Revision as of 07:20, 18 October 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zio_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zio_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 34:		Line 34:
	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-	*[[Pyrrolysyl-tRNA synthetase\|Pyrrolysyl-tRNA synthetase]]
	== References ==		== References ==
	<references/>		<references/>
Line 47:		Line 46:
	[[Category: Atp analogue]]		[[Category: Atp analogue]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
		+	[[Category: Cytoplasm]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]

OCA at 23:25, 4 August 2016

OCA — Thu, 04 Aug 2016 23:25:48 GMT

←Older revision		Revision as of 23:25, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP==		==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP==
	<StructureSection load='2zio' size='340' side='right' caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2zio' size='340' side='right' caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [http://www.ebi.ac.uk/pdbsum/2zio PDBsum], [http://www.topsan.org/Proteins/RSGI/2zio 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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [http://pdbe.org/2zio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [http://www.ebi.ac.uk/pdbsum/2zio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zio ProSAT], [http://www.topsan.org/Proteins/RSGI/2zio TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=2zio ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 2zio" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanosarcina mazei~~]]	+	[[Category: Dsm 2053]]
	[[Category: Ishii, R]]		[[Category: Ishii, R]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 13:58, 25 December 2014

OCA — Thu, 25 Dec 2014 13:58:35 GMT

←Older revision		Revision as of 13:58, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [http://www.ebi.ac.uk/pdbsum/2zio PDBsum], [http://www.topsan.org/Proteins/RSGI/2zio 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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [http://www.ebi.ac.uk/pdbsum/2zio PDBsum], [http://www.topsan.org/Proteins/RSGI/2zio 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 36:		Line 38:
	</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: Atp analogue]]		[[Category: Atp analogue]]
Line 51:		Line 53:
	[[Category: Pyrrolysine]]		[[Category: Pyrrolysine]]
	[[Category: Pyrrolysyl-trna synthetase]]		[[Category: Pyrrolysyl-trna synthetase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Trna]]		[[Category: Trna]]
	[[Category: Unnatural amino acid]]		[[Category: Unnatural amino acid]]

OCA at 07:54, 29 September 2014

OCA — Mon, 29 Sep 2014 07:54:20 GMT

←Older revision		Revision as of 07:54, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2zio.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP==
		+	<StructureSection load='2zio' size='340' side='right' caption='[[2zio]], [[Resolution\|resolution]] 2.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e3c\|2e3c]], [[2zcd\|2zcd]], [[2zce\|2zce]], [[2zin\|2zin]]</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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [http://www.ebi.ac.uk/pdbsum/2zio PDBsum], [http://www.topsan.org/Proteins/RSGI/2zio 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/zi/2zio_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 ==
		+	Pyrrolysyl-tRNA synthetase (PylRS) esterifies pyrrolysine to tRNA(Pyl). In this study, N(epsilon)-(tert-butyloxycarbonyl)-L-lysine (BocLys) and N(epsilon)-allyloxycarbonyl-L-lysine (AlocLys) were esterified to tRNA(Pyl) by PylRS. Crystal structures of a PylRS catalytic fragment complexed with BocLys and an ATP analog and with AlocLys-AMP revealed that PylRS requires an N(epsilon)-carbonyl group bearing a substituent with a certain size. A PylRS(Y384F) mutant obtained by random screening exhibited higher in vitro aminoacylation and in vivo amber suppression activities with BocLys, AlocLys, and pyrrolysine than those of the wild-type PylRS. Furthermore, the structure-based Y306A mutation of PylRS drastically increased the in vitro aminoacylation activity for N(epsilon)-benzyloxycarbonyl-L-lysine (ZLys). A PylRS with both the Y306A and Y384F mutations enabled the large-scale preparation (>10 mg per liter medium) of proteins site-specifically containing N(epsilon)-(o-azidobenzyloxycarbonyl)-L-lysine (AzZLys). The AzZLys-containing protein was labeled with a fluorescent probe, by Staudinger ligation.

-	~~{{STRUCTURE_2zio\| PDB=2zio \| SCENE= }}~~	+	Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.,Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S Chem Biol. 2008 Nov 24;15(11):1187-97. PMID:19022179<ref>PMID:19022179</ref>

-	~~===Crystal structure~~ of the ~~catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19022179}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2zio]] 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=2ZIO 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:019022179<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
	[[Category: Ishii, R.]]		[[Category: Ishii, R.]]

OCA at 17:32, 20 October 2012

OCA — Sat, 20 Oct 2012 17:32:22 GMT

←Older revision		Revision as of 17:32, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zio]] 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=2ZIO OCA].	+	[[2zio]] 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=2ZIO OCA].

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

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

OCA — Fri, 27 Jul 2012 01:12:47 GMT

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

←Older revision

Revision as of 01:12, 27 July 2012

OCA at 01:12, 27 July 2012

OCA — Fri, 27 Jul 2012 01:12:45 GMT

←Older revision		Revision as of 01:12, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2zio.png\|left\|200px]]		[[Image:2zio.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zio", 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_2zio\| PDB=2zio \| SCENE= }}		{{STRUCTURE_2zio\| PDB=2zio \| SCENE= }}

	===Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP===		===Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19022179}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19022179 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19022179}}		{{ABSTRACT_PUBMED_19022179}}

	==About this Structure==		==About this Structure==
-	~~2ZIO~~ 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=2ZIO OCA].	+	[[2zio]] 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=2ZIO OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
		+	*[[Pyrrolysyl-tRNA synthetase\|Pyrrolysyl-tRNA synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19022179~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019022179</ref><references group="xtra"/>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
	[[Category: Ishii, R.]]		[[Category: Ishii, R.]]
Line 32:		Line 24:
	[[Category: Atp analogue]]		[[Category: Atp analogue]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
-	[[Category: Cytoplasm]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
Line 46:		Line 37:
	[[Category: Trna]]		[[Category: Trna]]
	[[Category: Unnatural amino acid]]		[[Category: Unnatural amino acid]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:51:31 2010''

OCA at 08:42, 22 September 2010

OCA — Wed, 22 Sep 2010 08:42:32 GMT

←Older revision		Revision as of 08:42, 22 September 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2ZIO is a ~~[[Single protein]]~~ 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=2ZIO OCA].	+	2ZIO 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=2ZIO OCA].

	==Reference==		==Reference==
-	Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification., Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S, Chem Biol. 2008 Nov;15(11):1187-97. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19022179 19022179]~~	+	<ref group="xtra">PMID:19022179</ref><references group="xtra"/>
	[[Category: Methanosarcina mazei]]		[[Category: Methanosarcina mazei]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Ishii, R.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
		+	[[Category: Yanagisawa, T.]]
		+	[[Category: Yokoyama, S.]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Atp analogue]]		[[Category: Atp analogue]]
Line 45:		Line 47:
	[[Category: Unnatural amino acid]]		[[Category: Unnatural amino acid]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 10 20~~:03:~~14 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:51:31 2010''