2rd2 - Revision history

OCA at 09:21, 21 February 2024

2024-02-21T09:21:36Z

← Older revision		Revision as of 09:21, 21 February 2024
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	<StructureSection load='2rd2' size='340' side='right'caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2rd2' size='340' side='right'caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=QSI:5-O-[N~~-~~(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.6Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1qtq\|1qtq]], [[2re8\|2re8]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>glnS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18]~~ </~~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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [https://pdbe.org/2rd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd2 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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [https://pdbe.org/2rd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd2 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/SYQ_ECOLI SYQ_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2rd2 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=2rd2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Information transfer from nucleic acid to protein is mediated by aminoacyl-tRNA synthetases, which catalyze the specific pairings of amino acids with transfer RNAs. Despite copious sequence and structural information on the 22 tRNA synthetase families, little is known of the enzyme signatures that specify amino acid selectivities. Here, we show that transplanting a conserved arginine residue from glutamyl-tRNA synthetase (GluRS) to glutaminyl-tRNA synthetase (GlnRS) improves the K(M) of GlnRS for noncognate glutamate. Two crystal structures of this C229R GlnRS mutant reveal that a conserved twin-arginine GluRS amino acid identity signature cannot be incorporated into GlnRS without disrupting surrounding protein structural elements that interact with the tRNA. Consistent with these findings, we show that cumulative replacement of other primary binding site residues in GlnRS, with those of GluRS, only slightly improves the ability of the GlnRS active site to accommodate glutamate. However, introduction of 22 amino acid replacements and one deletion, including substitution of the entire primary binding site and two surface loops adjacent to the region disrupted in C229R, improves the capacity of Escherichia coli GlnRS to synthesize misacylated Glu-tRNA(Gln) by 16,000-fold. This hybrid enzyme recapitulates the function of misacylating GluRS enzymes found in organisms that synthesize Gln-tRNA(Gln) by an alternative pathway. These findings implicate the RNA component of the contemporary GlnRS-tRNA(Gln) complex in mediating amino acid specificity. This role for tRNA may persist as a relic of primordial cells in which the evolution of the genetic code was driven by RNA-catalyzed amino acid-RNA pairing.

	A rationally engineered misacylating aminoacyl-tRNA synthetase.,Bullock TL, Rodriguez-Hernandez A, Corigliano EM, Perona JJ Proc Natl Acad Sci U S A. 2008 May 27;105(21):7428-33. Epub 2008 May 13. PMID:18477696<ref>PMID:18477696</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2rd2" 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: ~~Ecoli~~]]		[[Category: Escherichia coli]]
	[[Category: ~~Glutamine~~-~~-tRNA ligase~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bullock~~, T L~~]]		[[Category: Bullock TL]]
	[[Category: Perona~~, J J]]~~		[[Category: Perona JJ]]
	~~[[Category: Aminoacyl-trna synthetase]]~~
	~~[[Category: Atp-binding]]~~
	~~[[Category: Ligase]]~~
	~~[[Category: Ligase-rna complex]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Protein biosynthesis]]~~
	~~[[Category: Protein-rna complex~~]]

OCA at 04:21, 2 July 2021

2021-07-02T04:21:55Z

← Older revision		Revision as of 04:21, 2 July 2021
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	==Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE==		==Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE==
	<StructureSection load='2rd2' size='340' side='right' caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2rd2' size='340' side='right'caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qtq\|1qtq]], [[2re8\|2re8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qtq\|1qtq]], [[2re8\|2re8]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [~~http~~://pdbe.org/2rd2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rd2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd2 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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [https://pdbe.org/2rd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd2 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]		*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Ecoli]]		[[Category: Ecoli]]
	[[Category: Glutamine--tRNA ligase]]		[[Category: Glutamine--tRNA ligase]]
			[[Category: Large Structures]]
	[[Category: Bullock, T L]]		[[Category: Bullock, T L]]
	[[Category: Perona, J J]]		[[Category: Perona, J J]]

OCA at 11:35, 5 September 2018

2018-09-05T11:35:59Z

← Older revision		Revision as of 11:35, 5 September 2018
Line 1:		Line 1:

	==Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE==		==Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE==
	<StructureSection load='2rd2' size='340' side='right' caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2rd2' size='340' side='right' caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://pdbe.org/2rd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://pdbe.org/2rd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd2 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rd2_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rd2_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 23:07, 9 February 2016

2016-02-09T23:07:56Z

← Older revision		Revision as of 23:07, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2rd2' size='340' side='right' caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2rd2' size='340' side='right' caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qtq\|1qtq]], [[2re8\|2re8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qtq\|1qtq]], [[2re8\|2re8]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://pdbe.org/2rd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=2rd2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2rd2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia coli~~]]		[[Category: Ecoli]]
	[[Category: Glutamine--tRNA ligase]]		[[Category: Glutamine--tRNA ligase]]
	[[Category: Bullock, T L]]		[[Category: Bullock, T L]]

OCA at 16:06, 19 January 2015

2015-01-19T16:06:50Z

← Older revision		Revision as of 16:06, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qtq\|1qtq]], [[2re8\|2re8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qtq\|1qtq]], [[2re8\|2re8]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 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 36:		Line 36:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Glutamine--tRNA ligase]]		[[Category: Glutamine--tRNA ligase]]
	[[Category: Bullock, T L.]]		[[Category: Bullock, T L]]
	[[Category: Perona, J J.]]		[[Category: Perona, J J]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 08:18, 29 September 2014

2014-09-29T08:18:17Z

← Older revision		Revision as of 08:18, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2rd2~~.~~png~~\|~~left~~\|~~200px~~]]		==Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE==
			<StructureSection load='2rd2' size='340' side='right' caption='[[2rd2]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2rd2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RD2 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QSI:5-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE'>QSI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qtq\|1qtq]], [[2re8\|2re8]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glnS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </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=2rd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd2 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/rd/2rd2_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 ==
			Information transfer from nucleic acid to protein is mediated by aminoacyl-tRNA synthetases, which catalyze the specific pairings of amino acids with transfer RNAs. Despite copious sequence and structural information on the 22 tRNA synthetase families, little is known of the enzyme signatures that specify amino acid selectivities. Here, we show that transplanting a conserved arginine residue from glutamyl-tRNA synthetase (GluRS) to glutaminyl-tRNA synthetase (GlnRS) improves the K(M) of GlnRS for noncognate glutamate. Two crystal structures of this C229R GlnRS mutant reveal that a conserved twin-arginine GluRS amino acid identity signature cannot be incorporated into GlnRS without disrupting surrounding protein structural elements that interact with the tRNA. Consistent with these findings, we show that cumulative replacement of other primary binding site residues in GlnRS, with those of GluRS, only slightly improves the ability of the GlnRS active site to accommodate glutamate. However, introduction of 22 amino acid replacements and one deletion, including substitution of the entire primary binding site and two surface loops adjacent to the region disrupted in C229R, improves the capacity of Escherichia coli GlnRS to synthesize misacylated Glu-tRNA(Gln) by 16,000-fold. This hybrid enzyme recapitulates the function of misacylating GluRS enzymes found in organisms that synthesize Gln-tRNA(Gln) by an alternative pathway. These findings implicate the RNA component of the contemporary GlnRS-tRNA(Gln) complex in mediating amino acid specificity. This role for tRNA may persist as a relic of primordial cells in which the evolution of the genetic code was driven by RNA-catalyzed amino acid-RNA pairing.

	~~{{STRUCTURE_2rd2\| PDB=2rd2 \| SCENE= }}~~		A rationally engineered misacylating aminoacyl-tRNA synthetase.,Bullock TL, Rodriguez-Hernandez A, Corigliano EM, Perona JJ Proc Natl Acad Sci U S A. 2008 May 27;105(21):7428-33. Epub 2008 May 13. PMID:18477696<ref>PMID:18477696</ref>

	~~===Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18477696}}~~

	~~==About this Structure==~~
	~~[[2rd2]] is~~ a ~~2 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2RD2 OCA].~~

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018477696<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Glutamine--tRNA ligase]]		[[Category: Glutamine--tRNA ligase]]

OCA at 15:28, 20 October 2012

2012-10-20T15:28:04Z

← Older revision		Revision as of 15:28, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2rd2]] is a 2 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA].		[[2rd2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA].

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

OCA: Protected "2rd2" [edit=sysop:move=sysop]

2012-07-26T18:28:22Z

Protected "2rd2" [edit=sysop:move=sysop]

← Older revision	Revision as of 18:28, 26 July 2012
(No difference)

OCA at 18:28, 26 July 2012

2012-07-26T18:28:20Z

← Older revision		Revision as of 18:28, 26 July 2012
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	~~{{Seed}}~~
	[[Image:2rd2.png\|left\|200px]]		[[Image:2rd2.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2rd2", 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_2rd2\| PDB=2rd2 \| SCENE= }}		{{STRUCTURE_2rd2\| PDB=2rd2 \| SCENE= }}

	===Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE===		===Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18477696}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18477696 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18477696}}		{{ABSTRACT_PUBMED_18477696}}

	==About this Structure==		==About this Structure==
	~~2RD2~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA].		[[2rd2]] is a 2 chain structure of [[Aminoacyl tRNA Synthetase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA].

			==See Also==
			*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18477696~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018477696</ref><references group="xtra"/>
	[[Category: Escherichia coli ~~k12~~]]		[[Category: Escherichia coli]]
	[[Category: Glutamine--tRNA ligase]]		[[Category: Glutamine--tRNA ligase]]
	[[Category: Bullock, T L.]]		[[Category: Bullock, T L.]]
Line 30:		Line 21:
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Ligase/rna complex]]		[[Category: Ligase-rna complex]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Protein biosynthesis]]		[[Category: Protein biosynthesis]]
	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:28:24 2009''~~

OCA at 11:28, 17 February 2009

2009-02-17T11:28:25Z

← Older revision		Revision as of 11:28, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2RD2 is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA].		2RD2 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD2 OCA].

	==Reference==		==Reference==
	~~A rationally engineered misacylating aminoacyl-tRNA synthetase., Bullock TL, Rodriguez-Hernandez A, Corigliano EM, Perona JJ, Proc Natl Acad Sci U S A. 2008 May 27;105(21):7428-33. Epub 2008 May 13.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18477696 18477696]~~		<ref group="xtra">PMID:18477696</ref><references group="xtra"/>
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
	[[Category: Glutamine--tRNA ligase]]		[[Category: Glutamine--tRNA ligase]]
	~~[[Category: Protein complex]]~~
	[[Category: Bullock, T L.]]		[[Category: Bullock, T L.]]
	[[Category: Perona, J J.]]		[[Category: Perona, J J.]]
Line 38:		Line 37:
	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug 6 10~~:02:~~02 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:28:24 2009''