4wj4 - Revision history

OCA at 09:01, 20 March 2024

OCA — Wed, 20 Mar 2024 09:01:45 GMT

←Older revision		Revision as of 09:01, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</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]] 3.294Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [https://pdbe.org/4wj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [https://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [https://pdbe.org/4wj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [https://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>		[https://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNAAsn, and instead synthesize asparagine from tRNAAsn-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNAAsn, and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNAAsn to form Asn-tRNAAsn for use in protein synthesis. ND-AspRS, GatCAB, and tRNAAsn may assemble in an approximately 400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNAAsn. We report the 3.7-A resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNAAsn molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNAAsn formation evolutionarily preceded the direct attachment of Asn to tRNAAsn, our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.
-
-	Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.,Suzuki T, Nakamura A, Kato K, Soll D, Tanaka I, Sheppard K, Yao M Proc Natl Acad Sci U S A. 2014 Dec 29. pii: 201423314. PMID:25548166<ref>PMID:25548166</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4wj4" style="background-color:#fffaf0;"></div>

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

OCA at 07:10, 7 April 2023

OCA — Fri, 07 Apr 2023 07:10:59 GMT

←Older revision		Revision as of 07:10, 7 April 2023
Line 3:		Line 3:
	<StructureSection load='4wj4' size='340' side='right'caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>		<StructureSection load='4wj4' size='340' side='right'caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wj3\|4wj3]]</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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [https://pdbe.org/4wj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [https://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS, PA0963 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [~~http~~://pdbe.org/4wj4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>	+	[https://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Kato, K]]	+	[[Category: Kato K]]
-	[[Category: Nakamura, A]]	+	[[Category: Nakamura A]]
-	[[Category: Suzuki, T]]	+	[[Category: Suzuki T]]
-	[[Category: Tanaka, I]]	+	[[Category: Tanaka I]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	~~[[Category: Aminoacylation]]~~	+
-	~~[[Category: Ligase-rna complex]]~~	+
-	~~[[Category: Non-discriminating aspr]]~~	+
-	~~[[Category: Trna~~]]	+

OCA at 07:55, 23 May 2019

OCA — Thu, 23 May 2019 07:55:36 GMT

←Older revision		Revision as of 07:55, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid==		==Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid==
-	<StructureSection load='4wj4' size='340' side='right' caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>	+	<StructureSection load='4wj4' size='340' side='right'caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wj3\|4wj3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wj3\|4wj3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS, PA0963 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [http://pdbe.org/4wj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [http://pdbe.org/4wj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 ProSAT]</span></td></tr>
Line 22:		Line 23:

	==See Also==		==See Also==
-	*[[~~TRNA~~\|~~TRNA~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
		+	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]

OCA at 16:51, 11 August 2016

OCA — Thu, 11 Aug 2016 16:51:12 GMT

←Older revision		Revision as of 16:51, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid==		==Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid==
	<StructureSection load='4wj4' size='340' side='right' caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>		<StructureSection load='4wj4' size='340' side='right' caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wj3\|4wj3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wj3\|4wj3]]</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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wj4 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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [http://pdbe.org/4wj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4wj4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA\|TRNA]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:26, 14 January 2015

OCA — Wed, 14 Jan 2015 07:26:49 GMT

←Older revision		Revision as of 07:26, 14 January 2015
Line 1:		Line 1:
-	==structure of ~~protein~~-tRNA ~~complex~~==	+	==Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid==
	<StructureSection load='4wj4' size='340' side='right' caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>		<StructureSection load='4wj4' size='340' side='right' caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>		[[http://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNAAsn, and instead synthesize asparagine from tRNAAsn-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNAAsn, and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNAAsn to form Asn-tRNAAsn for use in protein synthesis. ND-AspRS, GatCAB, and tRNAAsn may assemble in an approximately 400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNAAsn. We report the 3.7-A resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNAAsn molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNAAsn formation evolutionarily preceded the direct attachment of Asn to tRNAAsn, our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.
		+
		+	Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.,Suzuki T, Nakamura A, Kato K, Soll D, Tanaka I, Sheppard K, Yao M Proc Natl Acad Sci U S A. 2014 Dec 29. pii: 201423314. PMID:25548166<ref>PMID:25548166</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:56, 31 December 2014

OCA — Wed, 31 Dec 2014 14:56:00 GMT

←Older revision		Revision as of 14:56, 31 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==structure of protein-tRNA complex==
-		+	<StructureSection load='4wj4' size='340' side='right' caption='[[4wj4]], [[Resolution\|resolution]] 3.29Å' scene=''>
-	~~The entry~~ 4wj4 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4wj4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WJ4 FirstGlance]. <br>
-	~~Authors~~: ~~Suzuki, T~~.~~, Nakamura, A~~.~~, Kato, K~~.~~, Tanaka, I~~.~~, Yao, M~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wj3\|4wj3]]</td></tr>
-	~~Description~~: ~~structure of protein-tRNA complex~~	+	<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>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=4wj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wj4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wj4 PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Tanaka~~, I]]	+	</table>
-	[[~~Category~~: ~~Yao, M~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYDND_PSEAE SYDND_PSEAE]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.5 times more efficient at aminoacylating E.coli 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:16352843</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kato, K]]		[[Category: Kato, K]]
-	[[Category: Suzuki, T]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]
		+	[[Category: Suzuki, T]]
		+	[[Category: Tanaka, I]]
		+	[[Category: Yao, M]]
		+	[[Category: Aminoacylation]]
		+	[[Category: Ligase-rna complex]]
		+	[[Category: Non-discriminating aspr]]
		+	[[Category: Trna]]

OCA at 19:34, 24 December 2014

OCA — Wed, 24 Dec 2014 19:34:06 GMT

←Older revision		Revision as of 19:34, 24 December 2014
Line 6:		Line 6:

	Description: structure of protein-tRNA complex		Description: structure of protein-tRNA complex
		+	[[Category: Unreleased Structures]]
		+	[[Category: Tanaka, I]]
		+	[[Category: Yao, M]]
		+	[[Category: Kato, K]]
		+	[[Category: Suzuki, T]]
		+	[[Category: Nakamura, A]]

OCA at 10:29, 29 October 2014

OCA — Wed, 29 Oct 2014 10:29:22 GMT

←Older revision		Revision as of 10:29, 29 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4wj4 is ON HOLD	+	The entry 4wj4 is ON HOLD until Paper Publication

	Authors: Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M.		Authors: Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M.

	Description: structure of protein-tRNA complex		Description: structure of protein-tRNA complex

OCA: Protected "4wj4" [edit=sysop:move=sysop]

OCA — Wed, 08 Oct 2014 06:57:27 GMT

Protected "4wj4" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:57, 8 October 2014

OCA: New page: '''Unreleased structure''' The entry 4wj4 is ON HOLD Authors: Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M. Description: structure of protein-tRNA complex

OCA — Wed, 08 Oct 2014 06:57:26 GMT

New page: '''Unreleased structure''' The entry 4wj4 is ON HOLD Authors: Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M. Description: structure of protein-tRNA complex

New page

'''Unreleased structure'''

The entry 4wj4 is ON HOLD

Authors: Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M.

Description: structure of protein-tRNA complex