2zod - Revision history

OCA at 13:46, 1 November 2023

2023-11-01T13:46:18Z

←Older revision		Revision as of 13:46, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zod' size='340' side='right'caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2zod' size='340' side='right'caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex~~ aeolicus~~" huber and stetter 2001~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.98Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[2yye\|2yye]]~~, [[~~2zau~~\|~~2zau~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>selD, aq_1030 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~63363~~ "~~Aquifex aeolicus~~" ~~Huber and Stetter 2001])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3]~~ </~~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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [https://pdbe.org/2zod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [https://www.ebi.ac.uk/pdbsum/2zod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zod ProSAT], [https://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [https://pdbe.org/2zod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [https://www.ebi.ac.uk/pdbsum/2zod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zod ProSAT], [https://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes selenophosphate from selenide and ATP (By similarity).	+	[https://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE] Synthesizes selenophosphate from selenide and ATP (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus ~~huber and stetter 2001~~]]	+	[[Category: Aquifex aeolicus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Selenide, water dikinase]]~~	+	[[Category: Matsumoto E]]
-	[[Category: Matsumoto, E]]	+	[[Category: Sekine SI]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Yokoyama S]]
-	[[Category: Sekine~~, S I~~]]	+
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Full-length selenophosphate synthetase]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Selenium]]~~	+
-	~~[[Category: Selenocysteine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 17:34, 15 December 2021

2021-12-15T17:34:23Z

←Older revision		Revision as of 17:34, 15 December 2021
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	==Crystal structure of selenophosphate synthetase from Aquifex aeolicus==		==Crystal structure of selenophosphate synthetase from Aquifex aeolicus==
-	<StructureSection load='2zod' size='340' side='right' caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='2zod' size='340' side='right'caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zod]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZOD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yye\|2yye]], [[2zau\|2zau]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2yye\|2yye]], [[2zau\|2zau]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [~~http~~://pdbe.org/2zod PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zod PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zod ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [https://pdbe.org/2zod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [https://www.ebi.ac.uk/pdbsum/2zod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zod ProSAT], [https://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes selenophosphate from selenide and ATP (By similarity).	+	[[https://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes selenophosphate from selenide and ATP (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
		+	[[Category: Large Structures]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
	[[Category: Matsumoto, E]]		[[Category: Matsumoto, E]]

OCA at 06:59, 18 October 2018

2018-10-18T06:59:07Z

←Older revision		Revision as of 06:59, 18 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of selenophosphate synthetase from Aquifex aeolicus==		==Crystal structure of selenophosphate synthetase from Aquifex aeolicus==
	<StructureSection load='2zod' size='340' side='right' caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2zod' size='340' side='right' caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://pdbe.org/2zod PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://pdbe.org/2zod PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zod ProSAT], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zo/2zod_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zo/2zod_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 07:24, 8 February 2016

2016-02-08T07:24:58Z

←Older revision		Revision as of 07:24, 8 February 2016
Line 7:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://pdbe.org/2zod PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=2zod ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 2zod" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:37, 24 December 2014

2014-12-24T21:37:54Z

←Older revision		Revision as of 21:37, 24 December 2014
Line 9:		Line 9:
	<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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</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=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes selenophosphate from selenide and ATP (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
-	[[Category: Matsumoto, E.]]	+	[[Category: Matsumoto, E]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sekine, S I.]]	+	[[Category: Sekine, S I]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Full-length selenophosphate synthetase]]		[[Category: Full-length selenophosphate synthetase]]
Line 44:		Line 46:
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Selenium]]		[[Category: Selenium]]
	[[Category: Selenocysteine]]		[[Category: Selenocysteine]]
-	[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:28, 10 October 2014

2014-10-10T06:28:38Z

←Older revision		Revision as of 06:28, 10 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2zod\| PDB~~=2zod \| ~~SCENE~~= }}	+	==Crystal structure of selenophosphate synthetase from Aquifex aeolicus==
-	===~~Crystal~~ structure ~~of selenophosphate synthetase~~ from Aquifex aeolicus===	+	<StructureSection load='2zod' size='340' side='right' caption='[[2zod]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18773910}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZOD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yye\|2yye]], [[2zau\|2zau]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">selD, aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zod OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zod RCSB], [http://www.ebi.ac.uk/pdbsum/2zod PDBsum], [http://www.topsan.org/Proteins/RSGI/2zod TOPSAN]</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/zo/2zod_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 ==
		+	Selenophosphate synthetase (SPS) catalyzes the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential reactive selenium donor for the formation of selenocysteine (Sec) and 2-selenouridine residues in proteins and RNAs, respectively. Many SPS are themselves Sec-containing proteins, in which Sec replaces Cys in the catalytically essential position (Sec/Cys). We solved the crystal structures of Aquifex aeolicus SPS and its complex with adenosine 5'-(alpha,beta-methylene) triphosphate (AMPCPP). The ATP-binding site is formed at the subunit interface of the homodimer. Four Asp residues coordinate four metal ions to bind the phosphate groups of AMPCPP. In the free SPS structure, the two loop regions in the ATP-binding site are not ordered, and no enzyme-associated metal is observed. This suggests that ATP binding, metal binding, and the formation of their binding sites are interdependent. To identify the amino-acid residues that contribute to SPS activity, we prepared six mutants of SPS and examined their selenide-dependent ATP consumption. Mutational analyses revealed that Sec/Cys13 and Lys16 are essential. In SPS.AMPCPP, the N-terminal loop, including the two residues, assumes different conformations ("open" and "closed") between the two subunits. The AMPCPP gamma-phosphate group is solvent-accessible, suggesting that a putative nucleophile could attack the ATP gamma-phosphate group to generate selenophosphate and adenosine 5'-diphosphate (ADP). Selenide attached to Sec/Cys13 as -Se-Se(-)/-S-Se(-) could serve as the nucleophile in the "closed" conformation. A water molecule, fixed close to the beta-phosphate group, could function as the nucleophile in subsequent ADP hydrolysis to orthophosphate and adenosine 5'-monophosphate.

-	~~==Function==~~	+	Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.,Itoh Y, Sekine S, Matsumoto E, Akasaka R, Takemoto C, Shirouzu M, Yokoyama S J Mol Biol. 2009 Feb 6;385(5):1456-69. Epub 2008 Aug 26. PMID:18773910<ref>PMID:18773910</ref>
-	~~[[http://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes~~ selenophosphate ~~from selenide~~ and ~~ATP~~ (~~By similarity~~).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2zod]] is~~ a ~~2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:018773910</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]

OCA at 05:23, 9 April 2014

2014-04-09T05:23:27Z

←Older revision		Revision as of 05:23, 9 April 2014
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-	[[Image:2zod.png\|left\|200px]]
-
	{{STRUCTURE_2zod\| PDB=2zod \| SCENE= }}		{{STRUCTURE_2zod\| PDB=2zod \| SCENE= }}
-
	===Crystal structure of selenophosphate synthetase from Aquifex aeolicus===		===Crystal structure of selenophosphate synthetase from Aquifex aeolicus===
		+	{{ABSTRACT_PUBMED_18773910}}

-	~~{{ABSTRACT_PUBMED_18773910}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes selenophosphate from selenide and ATP (By similarity).

	==About this Structure==		==About this Structure==
-	[[2zod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus Aquifex~~ aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA].	+	[[2zod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:018773910</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018773910</ref><references group="xtra"/><references/>
-	[[Category: Aquifex aeolicus]]	+	[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
	[[Category: Matsumoto, E.]]		[[Category: Matsumoto, E.]]

OCA: Protected "2zod" [edit=sysop:move=sysop]

2013-01-07T22:48:52Z

Protected "2zod" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:48, 7 January 2013

OCA at 22:48, 7 January 2013

2013-01-07T22:48:48Z

←Older revision		Revision as of 22:48, 7 January 2013
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-	{{Seed}}
	[[Image:2zod.png\|left\|200px]]		[[Image:2zod.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zod", 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_2zod\| PDB=2zod \| SCENE= }}		{{STRUCTURE_2zod\| PDB=2zod \| SCENE= }}

	===Crystal structure of selenophosphate synthetase from Aquifex aeolicus===		===Crystal structure of selenophosphate synthetase from Aquifex aeolicus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18773910}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18773910 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18773910}}		{{ABSTRACT_PUBMED_18773910}}

	==About this Structure==		==About this Structure==
-	~~2ZOD~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA].	+	[[2zod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yyd 2yyd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18773910~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018773910</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
Line 43:		Line 31:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:10:27 2009''

OCA at 18:10, 16 February 2009

2009-02-16T18:10:28Z

←Older revision		Revision as of 18:10, 16 February 2009
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	==Reference==		==Reference==
-	Structure of Selenophosphate Synthetase Essential for Selenium Incorporation into Proteins and RNAs., Itoh Y, Sekine SI, Matsumoto E, Akasaka R, Takemoto C, Shirouzu M, Yokoyama S, J Mol Biol. 2008 Aug 26. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18773910 18773910]~~	+	<ref group="xtra">PMID:18773910</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
Line 44:		Line 44:
	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov~~ 16 18:04:~~49 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:10:27 2009''