4rra - Revision history

OCA at 12:55, 1 March 2024

OCA — Fri, 01 Mar 2024 12:55:06 GMT

←Older revision		Revision as of 12:55, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RRA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RRA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [https://pdbe.org/4rra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [https://www.ebi.ac.uk/pdbsum/4rra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra 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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [https://pdbe.org/4rra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [https://www.ebi.ac.uk/pdbsum/4rra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SYTE_AERPE SYTE_AERPE] Freestanding tRNA editing subunit of threonine--tRNA ligase, the catalytic subunit is probably AC Q9YDW0. Deacylates (edits) mischarged L-seryl-tRNA(Thr) in trans; has no activity on correctly charged L-threonyl-tRNA(Thr) (PubMed:26113036). Probably does not aminoacylate tRNA(Thr) (By similarity). Deacylates correctly charged glycyl-tRNA(Gly), but not glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH of tRNA adenine 76 has been dehydroxylated) nor the 2'-fluoro tRNA derivative, strongly suggesting the editing function is catalyzed by the 2'-OH of A76 of tRNA(Thr) (PubMed:26113036).[UniProtKB:Q980D1]<ref>PMID:26113036</ref>		[https://www.uniprot.org/uniprot/SYTE_AERPE SYTE_AERPE] Freestanding tRNA editing subunit of threonine--tRNA ligase, the catalytic subunit is probably AC Q9YDW0. Deacylates (edits) mischarged L-seryl-tRNA(Thr) in trans; has no activity on correctly charged L-threonyl-tRNA(Thr) (PubMed:26113036). Probably does not aminoacylate tRNA(Thr) (By similarity). Deacylates correctly charged glycyl-tRNA(Gly), but not glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH of tRNA adenine 76 has been dehydroxylated) nor the 2'-fluoro tRNA derivative, strongly suggesting the editing function is catalyzed by the 2'-OH of A76 of tRNA(Thr) (PubMed:26113036).[UniProtKB:Q980D1]<ref>PMID:26113036</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. We show, using three distinct archaea, that a side-chain-stripped recognition site is fully capable of solving a subtle discrimination problem. While biochemical probing establishes that RNA plays the catalytic role, mechanistic insights from multiple high-resolution snapshots reveal that differential remodelling of the catalytic core at the RNA-peptide interface provides the determinants for correct proofreading activity. The functional crosstalk between RNA and protein elucidated here suggests how primordial enzyme functions could have emerged on RNA-peptide scaffolds before recruitment of specific side chains.
-
-	Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.,Ahmad S, Muthukumar S, Kuncha SK, Routh SB, Yerabham AS, Hussain T, Kamarthapu V, Kruparani SP, Sankaranarayanan R Nat Commun. 2015 Jun 26;6:7552. doi: 10.1038/ncomms8552. PMID:26113036<ref>PMID:26113036</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rra" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:25, 8 March 2023

OCA — Wed, 08 Mar 2023 08:25:28 GMT

←Older revision		Revision as of 08:25, 8 March 2023
Line 1:		Line 1:

	==N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)==		==N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)==
-	<StructureSection load='4rra' size='340' side='right' caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4rra' size='340' side='right'caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aerpe Aerpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RRA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rr6\|4rr6]], [[4rr7\|4rr7]], [[4rr8\|4rr8]], [[4rr9\|4rr9]], [[4rrb\|4rrb]], [[4rrc\|4rrc]], [[4rrd\|4rrd]], [[4rrf\|4rrf]], [[4rrg\|4rrg]], [[4rrh\|4rrh]], [[4rri\|4rri]], [[4rrj\|4rrj]], [[4rrk\|4rrk]], [[4rrl\|4rrl]], [[4rrm\|4rrm]], [[4rrq\|4rrq]], [[4rrr\|4rrr]]</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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [https://pdbe.org/4rra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [https://www.ebi.ac.uk/pdbsum/4rra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thrS2, APE_0117.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [~~http~~://pdbe.org/4rra PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rra PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYTE_AERPE SYTE_AERPE] Freestanding tRNA editing subunit of threonine--tRNA ligase, the catalytic subunit is probably AC Q9YDW0. Deacylates (edits) mischarged L-seryl-tRNA(Thr) in trans; has no activity on correctly charged L-threonyl-tRNA(Thr) (PubMed:26113036). Probably does not aminoacylate tRNA(Thr) (By similarity). Deacylates correctly charged glycyl-tRNA(Gly), but not glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH of tRNA adenine 76 has been dehydroxylated) nor the 2'-fluoro tRNA derivative, strongly suggesting the editing function is catalyzed by the 2'-OH of A76 of tRNA(Thr) (PubMed:26113036).[UniProtKB:Q980D1]<ref>PMID:26113036</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aerpe~~]]	+	[[Category: Aeropyrum pernix K1]]
-	[[Category: ~~Threonine--tRNA ligase~~]]	+	[[Category: Large Structures]]
-	[[Category: Ahmad, S]]	+	[[Category: Ahmad S]]
-	[[Category: Kamarthapu, V]]	+	[[Category: Kamarthapu V]]
-	[[Category: Muthukumar, S]]	+	[[Category: Muthukumar S]]
-	[[Category: Sankaranarayanan, R]]	+	[[Category: Sankaranarayanan R]]
-	[[Category: Yerabham~~, A S.K]]~~	+	[[Category: Yerabham ASK]]
-	~~[[Category: Dtd-like fold]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Proofreading~~]]	+

OCA at 09:08, 22 November 2017

OCA — Wed, 22 Nov 2017 09:08:48 GMT

←Older revision		Revision as of 09:08, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4rra' size='340' side='right' caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4rra' size='340' side='right' caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RRA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rr6\|4rr6]], [[4rr7\|4rr7]], [[4rr8\|4rr8]], [[4rr9\|4rr9]], [[4rrb\|4rrb]], [[4rrc\|4rrc]], [[4rrd\|4rrd]], [[4rrf\|4rrf]], [[4rrg\|4rrg]], [[4rrh\|4rrh]], [[4rri\|4rri]], [[4rrj\|4rrj]], [[4rrk\|4rrk]], [[4rrl\|4rrl]], [[4rrm\|4rrm]], [[4rrq\|4rrq]], [[4rrr\|4rrr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rr6\|4rr6]], [[4rr7\|4rr7]], [[4rr8\|4rr8]], [[4rr9\|4rr9]], [[4rrb\|4rrb]], [[4rrc\|4rrc]], [[4rrd\|4rrd]], [[4rrf\|4rrf]], [[4rrg\|4rrg]], [[4rrh\|4rrh]], [[4rri\|4rri]], [[4rrj\|4rrj]], [[4rrk\|4rrk]], [[4rrl\|4rrl]], [[4rrm\|4rrm]], [[4rrq\|4rrq]], [[4rrr\|4rrr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thrS2, APE_0117.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [http://pdbe.org/4rra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [http://www.ebi.ac.uk/pdbsum/4rra PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra ProSAT]</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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [http://pdbe.org/4rra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [http://www.ebi.ac.uk/pdbsum/4rra PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aerpe]]
	[[Category: Threonine--tRNA ligase]]		[[Category: Threonine--tRNA ligase]]
	[[Category: Ahmad, S]]		[[Category: Ahmad, S]]

OCA at 13:24, 19 April 2017

OCA — Wed, 19 Apr 2017 13:24:14 GMT

←Older revision		Revision as of 13:24, 19 April 2017
Line 1:		Line 1:
		+
	==N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)==		==N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)==
	<StructureSection load='4rra' size='340' side='right' caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4rra' size='340' side='right' caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rr6\|4rr6]], [[4rr7\|4rr7]], [[4rr8\|4rr8]], [[4rr9\|4rr9]], [[4rrb\|4rrb]], [[4rrc\|4rrc]], [[4rrd\|4rrd]], [[4rrf\|4rrf]], [[4rrg\|4rrg]], [[4rrh\|4rrh]], [[4rri\|4rri]], [[4rrj\|4rrj]], [[4rrk\|4rrk]], [[4rrl\|4rrl]], [[4rrm\|4rrm]], [[4rrq\|4rrq]], [[4rrr\|4rrr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rr6\|4rr6]], [[4rr7\|4rr7]], [[4rr8\|4rr8]], [[4rr9\|4rr9]], [[4rrb\|4rrb]], [[4rrc\|4rrc]], [[4rrd\|4rrd]], [[4rrf\|4rrf]], [[4rrg\|4rrg]], [[4rrh\|4rrh]], [[4rri\|4rri]], [[4rrj\|4rrj]], [[4rrk\|4rrk]], [[4rrl\|4rrl]], [[4rrm\|4rrm]], [[4rrq\|4rrq]], [[4rrr\|4rrr]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [http://www.ebi.ac.uk/pdbsum/4rra 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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [http://pdbe.org/4rra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [http://www.ebi.ac.uk/pdbsum/4rra PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rra ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4rra" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:19, 15 July 2015

OCA — Wed, 15 Jul 2015 13:19:06 GMT

←Older revision		Revision as of 13:19, 15 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)==
		+	<StructureSection load='4rra' size='340' side='right' caption='[[4rra]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rra]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RRA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rr6\|4rr6]], [[4rr7\|4rr7]], [[4rr8\|4rr8]], [[4rr9\|4rr9]], [[4rrb\|4rrb]], [[4rrc\|4rrc]], [[4rrd\|4rrd]], [[4rrf\|4rrf]], [[4rrg\|4rrg]], [[4rrh\|4rrh]], [[4rri\|4rri]], [[4rrj\|4rrj]], [[4rrk\|4rrk]], [[4rrl\|4rrl]], [[4rrm\|4rrm]], [[4rrq\|4rrq]], [[4rrr\|4rrr]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=4rra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rra RCSB], [http://www.ebi.ac.uk/pdbsum/4rra PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. We show, using three distinct archaea, that a side-chain-stripped recognition site is fully capable of solving a subtle discrimination problem. While biochemical probing establishes that RNA plays the catalytic role, mechanistic insights from multiple high-resolution snapshots reveal that differential remodelling of the catalytic core at the RNA-peptide interface provides the determinants for correct proofreading activity. The functional crosstalk between RNA and protein elucidated here suggests how primordial enzyme functions could have emerged on RNA-peptide scaffolds before recruitment of specific side chains.

-	~~The entry 4rra is ON HOLD until Paper Publication~~	+	Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.,Ahmad S, Muthukumar S, Kuncha SK, Routh SB, Yerabham AS, Hussain T, Kamarthapu V, Kruparani SP, Sankaranarayanan R Nat Commun. 2015 Jun 26;6:7552. doi: 10.1038/ncomms8552. PMID:26113036<ref>PMID:26113036</ref>

-	~~Authors: Ahmad~~, S.~~, Muthukumar,~~ S.~~, Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	~~[[Category: Sankaranarayanan, R]]~~	+	__TOC__
-	~~[[Category: Muthukumar, S]]~~	+	</StructureSection>
-	[[Category: ~~Yerabham, A.S.K~~]]	+	[[Category: Threonine--tRNA ligase]]
	[[Category: Ahmad, S]]		[[Category: Ahmad, S]]
	[[Category: Kamarthapu, V]]		[[Category: Kamarthapu, V]]
		+	[[Category: Muthukumar, S]]
		+	[[Category: Sankaranarayanan, R]]
		+	[[Category: Yerabham, A S.K]]
		+	[[Category: Dtd-like fold]]
		+	[[Category: Ligase]]
		+	[[Category: Proofreading]]

OCA at 17:15, 24 December 2014

OCA — Wed, 24 Dec 2014 17:15:23 GMT

←Older revision		Revision as of 17:15, 24 December 2014
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	Description: N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)		Description: N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)
		+	[[Category: Unreleased Structures]]
		+	[[Category: Sankaranarayanan, R]]
		+	[[Category: Muthukumar, S]]
		+	[[Category: Yerabham, A.S.K]]
		+	[[Category: Ahmad, S]]
		+	[[Category: Kamarthapu, V]]

OCA at 06:45, 26 November 2014

OCA — Wed, 26 Nov 2014 06:45:20 GMT

←Older revision		Revision as of 06:45, 26 November 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rra is ON HOLD	+	The entry 4rra is ON HOLD until Paper Publication

	Authors: Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.		Authors: Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

	Description: N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)		Description: N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)

OCA: Protected "4rra" [edit=sysop:move=sysop]

OCA — Wed, 19 Nov 2014 11:31:24 GMT

Protected "4rra" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:31, 19 November 2014

OCA: New page: '''Unreleased structure''' The entry 4rra is ON HOLD Authors: Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R. Description: N-terminal editing domain o...

OCA — Wed, 19 Nov 2014 11:31:23 GMT

New page: '''Unreleased structure''' The entry 4rra is ON HOLD Authors: Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R. Description: N-terminal editing domain o...

New page

'''Unreleased structure'''

The entry 4rra is ON HOLD

Authors: Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

Description: N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)