3p8v - Revision history

OCA at 10:39, 21 February 2024

OCA — Wed, 21 Feb 2024 10:39:46 GMT

←Older revision		Revision as of 10:39, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3p8v' size='340' side='right'caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3p8v' size='340' side='right'caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus~~ abyssi~~" erauso et al. 1993~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P8V 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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]~~<~~/div></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~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])~~</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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [https://pdbe.org/3p8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [https://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v 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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [https://pdbe.org/3p8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [https://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9V228_PYRAB Q9V228_PYRAB]
-	~~Asparagine synthetase A (AsnA) catalyzes asparagine synthesis using aspartate, ATP, and ammonia as substrates. Asparagine is formed in two steps~~: the beta-carboxylate group of aspartate is first activated by ATP to form an aminoacyl-AMP before its amidation by a nucleophilic attack with an ammonium ion. Interestingly, this mechanism of amino acid activation resembles that used by aminoacyl-tRNA synthetases, which first activate the alpha-carboxylate group of the amino acid to form also an aminoacyl-AMP before they transfer the activated amino acid onto the cognate tRNA. In a previous investigation, we have shown that the open reading frame of Pyrococcus abyssi annotated as asparaginyl-tRNA synthetase (AsnRS) 2 is, in fact, an archaeal asparagine synthetase A (AS-AR) that evolved from an ancestral aspartyl-tRNA synthetase (AspRS). We present here the crystal structure of this AS-AR. The fold of this protein is similar to that of bacterial AsnA and resembles the catalytic cores of AspRS and AsnRS. The high-resolution structures of AS-AR associated with its substrates and end-products help to understand the reaction mechanism of asparagine formation and release. A comparison of the catalytic core of AS-AR with those of archaeal AspRS and AsnRS and with that of bacterial AsnA reveals a strong conservation. This study uncovers how the active site of the ancestral AspRS rearranged throughout evolution to transform an enzyme activating the alpha-carboxylate group into an enzyme that is able to activate the beta-carboxylate group of aspartate, which can react with ammonia instead of tRNA.	+
-		+
-	Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.,Blaise M, Frechin M, Olieric V, Charron C, Sauter C, Lorber B, Roy H, Kern D J Mol Biol. 2011 Sep 23;412(3):437-52. Epub 2011 Jul 28. PMID:21820443<ref>PMID:21820443</~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3p8v" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Blaise, M~~]]	+	[[Category: Pyrococcus abyssi]]
-	[[Category: ~~Kern, D~~]]	+	[[Category: Blaise M]]
-	[[Category: ~~Ammonium]]~~	+	[[Category: Kern D]]
-	~~[[Category: Amp]]~~	+
-	~~[[Category: Anti-parallel beta sheet]]~~	+
-	~~[[Category: Asn]]~~	+
-	~~[[Category: Asp]]~~	+
-	~~[[Category: Asparagine synthetase]]~~	+
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Synthetase~~]]	+

OCA at 08:29, 25 May 2022

OCA — Wed, 25 May 2022 08:29:32 GMT

←Older revision		Revision as of 08:29, 25 May 2022
Line 1:		Line 1:

	==Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid==		==Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid==
-	<StructureSection load='3p8v' size='340' side='right' caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3p8v' size='340' side='right'caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3P8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P8V 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">[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [~~http~~://pdbe.org/3p8v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v 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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [https://pdbe.org/3p8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [https://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus abyssi erauso et al. 1993]]		[[Category: Pyrococcus abyssi erauso et al. 1993]]
		+	[[Category: Large Structures]]
	[[Category: Blaise, M]]		[[Category: Blaise, M]]
	[[Category: Kern, D]]		[[Category: Kern, D]]

OCA at 01:12, 5 August 2016

OCA — Fri, 05 Aug 2016 01:12:44 GMT

←Older revision		Revision as of 01:12, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid==		==Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid==
	<StructureSection load='3p8v' size='340' side='right' caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3p8v' size='340' side='right' caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_abyssi Pyrococcus~~ abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P8V 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">[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [http://www.ebi.ac.uk/pdbsum/3p8v 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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [http://pdbe.org/3p8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [http://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v 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 3p8v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus abyssi]]	+	[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: Blaise, M]]		[[Category: Blaise, M]]
	[[Category: Kern, D]]		[[Category: Kern, D]]

OCA at 22:26, 3 January 2015

OCA — Sat, 03 Jan 2015 22:26:41 GMT

←Older revision		Revision as of 22:26, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P8V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene><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>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi])</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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [http://www.ebi.ac.uk/pdbsum/3p8v 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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [http://www.ebi.ac.uk/pdbsum/3p8v PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.,Blaise M, Frechin M, Olieric V, Charron C, Sauter C, Lorber B, Roy H, Kern D J Mol Biol. 2011 Sep 23;412(3):437-52. Epub 2011 Jul 28. PMID:21820443<ref>PMID:21820443</ref>		Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.,Blaise M, Frechin M, Olieric V, Charron C, Sauter C, Lorber B, Roy H, Kern D J Mol Biol. 2011 Sep 23;412(3):437-52. Epub 2011 Jul 28. PMID:21820443<ref>PMID:21820443</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
-	[[Category: Blaise, M.]]	+	[[Category: Blaise, M]]
-	[[Category: Kern, D.]]	+	[[Category: Kern, D]]
	[[Category: Ammonium]]		[[Category: Ammonium]]
	[[Category: Amp]]		[[Category: Amp]]

OCA at 05:20, 4 June 2014

OCA — Wed, 04 Jun 2014 05:20:56 GMT

←Older revision		Revision as of 05:20, 4 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3p8v.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid==
		+	<StructureSection load='3p8v' size='340' side='right' caption='[[3p8v]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P8V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3p8t\|3p8t]], [[3p8y\|3p8y]], [[3reu\|3reu]], [[3rex\|3rex]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi])</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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [http://www.ebi.ac.uk/pdbsum/3p8v PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Asparagine synthetase A (AsnA) catalyzes asparagine synthesis using aspartate, ATP, and ammonia as substrates. Asparagine is formed in two steps: the beta-carboxylate group of aspartate is first activated by ATP to form an aminoacyl-AMP before its amidation by a nucleophilic attack with an ammonium ion. Interestingly, this mechanism of amino acid activation resembles that used by aminoacyl-tRNA synthetases, which first activate the alpha-carboxylate group of the amino acid to form also an aminoacyl-AMP before they transfer the activated amino acid onto the cognate tRNA. In a previous investigation, we have shown that the open reading frame of Pyrococcus abyssi annotated as asparaginyl-tRNA synthetase (AsnRS) 2 is, in fact, an archaeal asparagine synthetase A (AS-AR) that evolved from an ancestral aspartyl-tRNA synthetase (AspRS). We present here the crystal structure of this AS-AR. The fold of this protein is similar to that of bacterial AsnA and resembles the catalytic cores of AspRS and AsnRS. The high-resolution structures of AS-AR associated with its substrates and end-products help to understand the reaction mechanism of asparagine formation and release. A comparison of the catalytic core of AS-AR with those of archaeal AspRS and AsnRS and with that of bacterial AsnA reveals a strong conservation. This study uncovers how the active site of the ancestral AspRS rearranged throughout evolution to transform an enzyme activating the alpha-carboxylate group into an enzyme that is able to activate the beta-carboxylate group of aspartate, which can react with ammonia instead of tRNA.

-	<!--	+	Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.,Blaise M, Frechin M, Olieric V, Charron C, Sauter C, Lorber B, Roy H, Kern D J Mol Biol. 2011 Sep 23;412(3):437-52. Epub 2011 Jul 28. PMID:21820443<ref>PMID:21820443</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3p8v"~~, ~~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_3p8v\| PDB=3p8v \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~archaeal asparagine synthetase A complexed with L-Aspartic acid===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21820443}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21820443 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21820443}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3p8v]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021820443<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Blaise, M.]]		[[Category: Blaise, M.]]

OCA at 04:56, 21 September 2011

OCA — Wed, 21 Sep 2011 04:56:15 GMT

←Older revision		Revision as of 04:56, 21 September 2011
Line 1:		Line 1:
-	[[Image:3p8v.~~jpg~~\|left\|200px]]	+	[[Image:3p8v.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid===		===Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21820443}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21820443 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21820443}}

	==About this Structure==		==About this Structure==
	[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA].		[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021820443</ref><references group="xtra"/>
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Blaise, M.]]		[[Category: Blaise, M.]]

OCA at 06:28, 17 August 2011

OCA — Wed, 17 Aug 2011 06:28:16 GMT

←Older revision		Revision as of 06:28, 17 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3p8v.jpg\|left\|200px]]

-	The ~~entry 3p8v~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3p8v", 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_3p8v\| PDB=3p8v \| SCENE= }}

-	~~Authors: Blaise, M., Kern, D.~~	+	===Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid===

-	~~Description: Protein~~ structure	+
		+	==About this Structure==
		+	[[3p8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA].
		+	[[Category: Pyrococcus abyssi]]
		+	[[Category: Blaise, M.]]
		+	[[Category: Kern, D.]]
		+	[[Category: Ammonium]]
		+	[[Category: Amp]]
		+	[[Category: Anti-parallel beta sheet]]
		+	[[Category: Asn]]
		+	[[Category: Asp]]
		+	[[Category: Asparagine synthetase]]
		+	[[Category: Atp binding]]
		+	[[Category: Ligase]]
		+	[[Category: Synthetase]]

OCA: Protected "3p8v" [edit=sysop:move=sysop]

OCA — Wed, 19 Jan 2011 05:47:40 GMT

Protected "3p8v" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:47, 19 January 2011

OCA at 05:47, 19 January 2011

OCA — Wed, 19 Jan 2011 05:47:39 GMT

←Older revision		Revision as of 05:47, 19 January 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3p8v is ON HOLD	+	The entry 3p8v is ON HOLD until Paper Publication

	Authors: Blaise, M., Kern, D.		Authors: Blaise, M., Kern, D.

	Description: Protein structure		Description: Protein structure
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 3 10:06:09 2010''

OCA: New page: '''Unreleased structure''' The entry 3p8v is ON HOLD Authors: Blaise, M., Kern, D. Description: Protein structure ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 3 1...

OCA — Wed, 03 Nov 2010 06:55:29 GMT

New page: '''Unreleased structure''' The entry 3p8v is ON HOLD Authors: Blaise, M., Kern, D. Description: Protein structure ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 3 1...

New page

'''Unreleased structure'''

The entry 3p8v is ON HOLD

Authors: Blaise, M., Kern, D.

Description: Protein structure

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 3 10:06:09 2010''