1zq1 - Revision history

OCA at 08:12, 15 May 2024

OCA — Wed, 15 May 2024 08:12:18 GMT

←Older revision		Revision as of 08:12, 15 May 2024
Line 3:		Line 3:
	<StructureSection load='1zq1' size='340' side='right'caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1zq1' size='340' side='right'caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZQ1 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]] 3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">gatD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), gatE ([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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [https://pdbe.org/1zq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1zq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zq1 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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [https://pdbe.org/1zq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1zq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GATD_PYRAB GATD_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity). [[https://www.uniprot.org/uniprot/GATE_PYRAB GATE_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity).	+	[https://www.uniprot.org/uniprot/GATD_PYRAB GATD_PYRAB] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blanquet, S]]	+	[[Category: Pyrococcus abyssi]]
-	[[Category: Mechulam, Y]]	+	[[Category: Blanquet S]]
-	[[Category: Panvert, M]]	+	[[Category: Mechulam Y]]
-	[[Category: Schmitt, E]]	+	[[Category: Panvert M]]
-	~~[[Category: 3d structure]]~~	+	[[Category: Schmitt E]]
-	~~[[Category: Asparaginase 1 family]]~~	+
-	~~[[Category: Gatd subfamily]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: X-ray~~]]	+

OCA at 08:14, 27 January 2021

OCA — Wed, 27 Jan 2021 08:14:48 GMT

←Older revision		Revision as of 08:14, 27 January 2021
Line 1:		Line 1:

	==Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi==		==Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi==
-	<StructureSection load='1zq1' size='340' side='right' caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1zq1' size='340' side='right'caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ZQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZQ1 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatD ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), gatE ([~~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">gatD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), gatE ([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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [~~http~~://pdbe.org/1zq1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1zq1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1zq1 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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [https://pdbe.org/1zq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1zq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GATD_PYRAB GATD_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity). [[~~http~~://www.uniprot.org/uniprot/GATE_PYRAB GATE_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity).	+	[[https://www.uniprot.org/uniprot/GATD_PYRAB GATD_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity). [[https://www.uniprot.org/uniprot/GATE_PYRAB GATE_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 1zq1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1zq1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamyl-tRNA(Gln) amidotransferase\|Glutamyl-tRNA(Gln) amidotransferase]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus abyssi erauso et al. 1993]]		[[Category: Pyrococcus abyssi erauso et al. 1993]]
		+	[[Category: Large Structures]]
	[[Category: Blanquet, S]]		[[Category: Blanquet, S]]
	[[Category: Mechulam, Y]]		[[Category: Mechulam, Y]]

OCA at 09:28, 2 May 2018

OCA — Wed, 02 May 2018 09:28:09 GMT

←Older revision		Revision as of 09:28, 2 May 2018
Line 1:		Line 1:
		+
	==Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi==		==Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi==
	<StructureSection load='1zq1' size='340' side='right' caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1zq1' size='340' side='right' caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), gatE ([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">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), gatE ([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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://pdbe.org/1zq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://pdbe.org/1zq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zq/1zq1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zq/1zq1_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:31, 8 February 2016

OCA — Mon, 08 Feb 2016 03:31:46 GMT

←Older revision		Revision as of 03:31, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1zq1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:27, 10 September 2015

OCA — Thu, 10 Sep 2015 07:27:16 GMT

←Older revision		Revision as of 07:27, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1zq1' size='340' side='right' caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1zq1' size='340' side='right' caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZQ1 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi]), gatE ([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">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), gatE ([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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://pdbe.org/1zq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1zq1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus abyssi]]	+	[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: Blanquet, S]]		[[Category: Blanquet, S]]
	[[Category: Mechulam, Y]]		[[Category: Mechulam, Y]]

OCA at 20:15, 24 December 2014

OCA — Wed, 24 Dec 2014 20:15:44 GMT

←Older revision		Revision as of 20:15, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZQ1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZQ1 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>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi]), gatE ([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">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi]), gatE ([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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GATD_PYRAB GATD_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity). [[http://www.uniprot.org/uniprot/GATE_PYRAB GATE_PYRAB]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
-	[[Category: Blanquet, S.]]	+	[[Category: Blanquet, S]]
-	[[Category: Mechulam, Y.]]	+	[[Category: Mechulam, Y]]
-	[[Category: Panvert, M.]]	+	[[Category: Panvert, M]]
-	[[Category: Schmitt, E.]]	+	[[Category: Schmitt, E]]
	[[Category: 3d structure]]		[[Category: 3d structure]]
	[[Category: Asparaginase 1 family]]		[[Category: Asparaginase 1 family]]

OCA at 00:36, 30 September 2014

OCA — Tue, 30 Sep 2014 00:36:52 GMT

←Older revision		Revision as of 00:36, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1zq1.~~png~~\|~~left~~\|200px]]	+	==Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi==
		+	<StructureSection load='1zq1' size='340' side='right' caption='[[1zq1]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1zq1]] is a 4 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=1ZQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZQ1 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>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi]), gatE ([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=1zq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zq1 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zq/1zq1_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gln) is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNA(Gln) is then matured into Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase-that of GatDE from Pyrococcus abyssi. The 3.0 A resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE.

-	~~{{STRUCTURE_1zq1\| PDB=1zq1 \| SCENE= }}~~	+	Structural basis for tRNA-dependent amidotransferase function.,Schmitt E, Panvert M, Blanquet S, Mechulam Y Structure. 2005 Oct;13(10):1421-33. PMID:16216574<ref>PMID:16216574</ref>

-	~~===Structure~~ of ~~GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16216574}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1zq1]] is a 4 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=1ZQ1 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016216574<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Blanquet, S.]]		[[Category: Blanquet, S.]]

OCA: Protected "1zq1" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:53:43 GMT

Protected "1zq1" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:53, 5 January 2013

OCA at 17:53, 5 January 2013

OCA — Sat, 05 Jan 2013 17:53:41 GMT

←Older revision		Revision as of 17:53, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1zq1.png\|left\|200px]]		[[Image:1zq1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1zq1", 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_1zq1\| PDB=1zq1 \| SCENE= }}		{{STRUCTURE_1zq1\| PDB=1zq1 \| SCENE= }}

	===Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi===		===Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16216574}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16216574 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16216574}}		{{ABSTRACT_PUBMED_16216574}}

	==About this Structure==		==About this Structure==
-	~~1ZQ1~~ is a 4 ~~chains~~ structure ~~of sequences~~ 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=1ZQ1 OCA].	+	[[1zq1]] is a 4 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=1ZQ1 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16216574~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016216574</ref><references group="xtra"/>
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Blanquet, S.]]		[[Category: Blanquet, S.]]
Line 32:		Line 20:
	[[Category: Asparaginase 1 family]]		[[Category: Asparaginase 1 family]]
	[[Category: Gatd subfamily]]		[[Category: Gatd subfamily]]
		+	[[Category: Lyase]]
	[[Category: X-ray]]		[[Category: X-ray]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:29:52 2009''

OCA at 16:29, 16 February 2009

OCA — Mon, 16 Feb 2009 16:29:53 GMT

←Older revision		Revision as of 16:29, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1ZQ1 is a ~~[[Protein complex]]~~ structure of sequences 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=1ZQ1 OCA].	+	1ZQ1 is a 4 chains structure of sequences 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=1ZQ1 OCA].

	==Reference==		==Reference==
-	~~Structural basis for tRNA-dependent amidotransferase function., Schmitt E, Panvert M, Blanquet S, Mechulam Y, Structure. 2005 Oct;13(10):1421-33.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16216574 16216574]~~	+	<ref group="xtra">PMID:16216574</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Blanquet, S.]]		[[Category: Blanquet, S.]]
Line 35:		Line 34:
	[[Category: X-ray]]		[[Category: X-ray]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 22~~:42:~~23 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:29:52 2009''