5gro - Revision history

OCA at 11:40, 2 August 2023

OCA — Wed, 02 Aug 2023 11:40:23 GMT

←Older revision		Revision as of 11:40, 2 August 2023
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	<StructureSection load='5gro' size='340' side='right'caption='[[5gro]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5gro' size='340' side='right'caption='[[5gro]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gro]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GRO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gro]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GRO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=85962 Campylobacter pylori])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Aspartate--tRNA(Asn)_ligase Aspartate--tRNA(Asn) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.23 6.1.1.23]~~ </~~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=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [https://pdbe.org/5gro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [https://www.ebi.ac.uk/pdbsum/5gro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [~~http~~://pdbe.org/5gro PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gro PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SYDND_HELPY SYDND_HELPY]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).<ref>PMID:16800632</ref>	+	[https://www.uniprot.org/uniprot/SYDND_HELPY SYDND_HELPY] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).<ref>PMID:16800632</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, C J]]	+	[[Category: Chen C-J]]
-	[[Category: Chuawong, P]]	+	[[Category: Chuawong P]]
-	[[Category: Fuengfuloy, P]]	+	[[Category: Fuengfuloy P]]
-	[[Category: Songsiriritthigul, C]]	+	[[Category: Songsiriritthigul C]]
-	[[Category: Suebka, S]]	+	[[Category: Suebka S]]
-	~~[[Category: Anticodon-binding domain]]~~	+
-	~~[[Category: Helicobacter pylori]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Non-discriminating aspartyl-trna synthetase~~]]	+

OCA at 06:50, 13 May 2020

OCA — Wed, 13 May 2020 06:50:50 GMT

←Older revision		Revision as of 06:50, 13 May 2020
Line 1:		Line 1:

	==Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori==		==Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori==
-	<StructureSection load='5gro' size='340' side='right' caption='[[5gro]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5gro' size='340' side='right'caption='[[5gro]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gro]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GRO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gro]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GRO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate--tRNA(Asn)_ligase Aspartate--tRNA(Asn) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.23 6.1.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate--tRNA(Asn)_ligase Aspartate--tRNA(Asn) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.23 6.1.1.23] </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=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [http://pdbe.org/5gro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [http://www.ebi.ac.uk/pdbsum/5gro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [http://pdbe.org/5gro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [http://www.ebi.ac.uk/pdbsum/5gro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5gro" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gro" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori]]
		+	[[Category: Large Structures]]
	[[Category: Chen, C J]]		[[Category: Chen, C J]]
	[[Category: Chuawong, P]]		[[Category: Chuawong, P]]

OCA at 08:03, 9 March 2017

OCA — Thu, 09 Mar 2017 08:03:59 GMT

←Older revision		Revision as of 08:03, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gro is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori==
		+	<StructureSection load='5gro' size='340' side='right' caption='[[5gro]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gro]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GRO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate--tRNA(Asn)_ligase Aspartate--tRNA(Asn) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.23 6.1.1.23] </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=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [http://pdbe.org/5gro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [http://www.ebi.ac.uk/pdbsum/5gro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYDND_HELPY SYDND_HELPY]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).<ref>PMID:16800632</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1-104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 A resolution. The apo form of H. pylori ND-AspRS1-104 shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing recognition elements to be proposed for tRNAAsp and tRNAAsn. It is proposed that a long loop (Arg77-Lys90) in this H. pylori domain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D-AspRS from E. coli and ND-AspRS from P. aeruginosa suggests that turns E and F (78GAGL81 and 83NPKL86) in H. pylori ND-AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNAAsp (34GUC36) and tRNAAsn (34GUU36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.

-	~~Authors~~:	+	Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori.,Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P Acta Crystallogr F Struct Biol Commun. 2017 Feb 1;73(Pt 2):62-69. doi:, 10.1107/S2053230X16020586. Epub 2017 Jan 19. PMID:28177315<ref>PMID:28177315</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5gro" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, C J]]
		+	[[Category: Chuawong, P]]
		+	[[Category: Fuengfuloy, P]]
		+	[[Category: Songsiriritthigul, C]]
		+	[[Category: Suebka, S]]
		+	[[Category: Anticodon-binding domain]]
		+	[[Category: Helicobacter pylori]]
		+	[[Category: Ligase]]
		+	[[Category: Non-discriminating aspartyl-trna synthetase]]

OCA: Protected "5gro" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 11:59:31 GMT

Protected "5gro" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:59, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gro is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Sep 2016 11:59:30 GMT

New page: '''Unreleased structure''' The entry 5gro is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5gro is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]