2znj - Revision history

OCA at 13:58, 13 March 2024

2024-03-13T13:58:03Z

←Older revision		Revision as of 13:58, 13 March 2024
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	<StructureSection load='2znj' size='340' side='right'caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2znj' size='340' side='right'caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Desha Desha~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>
-	</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~~=49338 DESHA])</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [https://pdbe.org/2znj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [https://www.ebi.ac.uk/pdbsum/2znj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2znj ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [https://pdbe.org/2znj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [https://www.ebi.ac.uk/pdbsum/2znj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2znj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B0S4P3_DESHA B0S4P3_DESHA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</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=2znj 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=2znj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pyrrolysine (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality.
-
-	Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality.,Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O Nature. 2009 Feb 26;457(7233):1163-7. Epub 2008 Dec 31. PMID:19118381<ref>PMID:19118381</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2znj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]		*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desha~~]]	+	[[Category: Desulfitobacterium hafniense]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Araiso, Y]]	+	[[Category: Araiso Y]]
-	[[Category: Ishitani, R]]	+	[[Category: Ishitani R]]
-	[[Category: Nozawa, K]]	+	[[Category: Nozawa K]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	[[Category: Soll, D]]	+	[[Category: Soll D]]
-	~~[[Category: Ligase~~]]	+

OCA at 17:33, 15 December 2021

2021-12-15T17:33:30Z

←Older revision		Revision as of 17:33, 15 December 2021
Line 1:		Line 1:

	==Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense==		==Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense==
-	<StructureSection load='2znj' size='340' side='right' caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2znj' size='340' side='right'caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Desha Desha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Desha Desha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>
-	</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=49338 DESHA])</td></tr>	+	</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=49338 DESHA])</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=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [~~http~~://pdbe.org/2znj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2znj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2znj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [https://pdbe.org/2znj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [https://www.ebi.ac.uk/pdbsum/2znj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2znj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 29:

	==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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Desha]]		[[Category: Desha]]
		+	[[Category: Large Structures]]
	[[Category: Araiso, Y]]		[[Category: Araiso, Y]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 06:55, 18 October 2018

2018-10-18T06:55:03Z

←Older revision		Revision as of 06:55, 18 October 2018
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zn/2znj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zn/2znj_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 14:17, 11 August 2016

2016-08-11T14:17:32Z

←Older revision		Revision as of 14:17, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense==		==Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense==
	<StructureSection load='2znj' size='340' side='right' caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2znj' size='340' side='right' caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfitobacterium_hafniense Desulfitobacterium hafniense~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Desha Desha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>
-	</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=49338 ~~Desulfitobacterium hafniense~~])</td></tr>	+	</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=49338 DESHA])</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=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [http://www.ebi.ac.uk/pdbsum/2znj PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [http://pdbe.org/2znj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [http://www.ebi.ac.uk/pdbsum/2znj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2znj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<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=2znj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 26:
	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 2znj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfitobacterium hafniense~~]]	+	[[Category: Desha]]
	[[Category: Araiso, Y]]		[[Category: Araiso, Y]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 07:48, 20 January 2015

2015-01-20T07:48:01Z

←Older revision		Revision as of 07:48, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>
-	</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=49338 Desulfitobacterium hafniense])</td></tr>	+	</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=49338 Desulfitobacterium hafniense])</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=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [http://www.ebi.ac.uk/pdbsum/2znj PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [http://www.ebi.ac.uk/pdbsum/2znj PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Desulfitobacterium hafniense]]		[[Category: Desulfitobacterium hafniense]]
-	[[Category: Araiso, Y.]]	+	[[Category: Araiso, Y]]
-	[[Category: Ishitani, R.]]	+	[[Category: Ishitani, R]]
-	[[Category: Nozawa, K.]]	+	[[Category: Nozawa, K]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: Soll, D.]]	+	[[Category: Soll, D]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 06:23, 29 September 2014

2014-09-29T06:23:30Z

←Older revision		Revision as of 06:23, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2znj.~~png\|left~~\|200px]]	+	==Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense==
		+	<StructureSection load='2znj' size='340' side='right' caption='[[2znj]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2znj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZNJ FirstGlance]. <br>
		+	</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=49338 Desulfitobacterium hafniense])</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=2znj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2znj RCSB], [http://www.ebi.ac.uk/pdbsum/2znj PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zn/2znj_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 (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality.

-	~~{{STRUCTURE_2znj\| PDB=2znj \| SCENE= }}~~	+	Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality.,Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O Nature. 2009 Feb 26;457(7233):1163-7. Epub 2008 Dec 31. PMID:19118381<ref>PMID:19118381</ref>

-	~~===Crystal structure~~ of ~~Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19118381}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2znj]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019118381<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Desulfitobacterium hafniense]]		[[Category: Desulfitobacterium hafniense]]
	[[Category: Araiso, Y.]]		[[Category: Araiso, Y.]]

OCA at 20:20, 20 October 2012

2012-10-20T20:20:24Z

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

	==About this Structure==		==About this Structure==
-	[[2znj]] is a 3 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].	+	[[2znj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].

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

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

2012-07-27T10:08:38Z

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

←Older revision

Revision as of 10:08, 27 July 2012

OCA at 10:08, 27 July 2012

2012-07-27T10:08:36Z

←Older revision		Revision as of 10:08, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2znj.png\|left\|200px]]		[[Image:2znj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2znj", 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_2znj\| PDB=2znj \| SCENE= }}		{{STRUCTURE_2znj\| PDB=2znj \| SCENE= }}

	===Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense===		===Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19118381}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19118381 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19118381}}		{{ABSTRACT_PUBMED_19118381}}

	==About this Structure==		==About this Structure==
-	~~2ZNJ~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].	+	[[2znj]] is a 3 chain structure of [[Aminoacyl tRNA Synthetase]] with sequence from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19118381~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019118381</ref><references group="xtra"/>
	[[Category: Desulfitobacterium hafniense]]		[[Category: Desulfitobacterium hafniense]]
	[[Category: Araiso, Y.]]		[[Category: Araiso, Y.]]
Line 31:		Line 22:
	[[Category: Soll, D.]]		[[Category: Soll, D.]]
	[[Category: Ligase]]		[[Category: Ligase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:28:27 2010''

OCA at 08:19, 22 September 2010

2010-09-22T08:19:29Z

←Older revision		Revision as of 08:19, 22 September 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2ZNJ is a ~~[[Single protein]]~~ structure ~~of sequence~~ from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].	+	2ZNJ is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense Desulfitobacterium hafniense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNJ OCA].

	==Reference==		==Reference==
-	Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality., Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O, Nature. 2009 Feb 26;457(7233):1163-7. Epub 2008 Dec 31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19118381 19118381]~~	+	<ref group="xtra">PMID:19118381</ref><references group="xtra"/>
	[[Category: Desulfitobacterium hafniense]]		[[Category: Desulfitobacterium hafniense]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Araiso, Y.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Ishitani, R.]]
		+	[[Category: Nozawa, K.]]
		+	[[Category: Nureki, O.]]
		+	[[Category: Soll, D.]]
	[[Category: Ligase]]		[[Category: Ligase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 20:~~11:~~58 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:28:27 2010''