2yye - Revision history

OCA at 09:11, 25 October 2023

OCA — Wed, 25 Oct 2023 09:11:26 GMT

←Older revision		Revision as of 09:11, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2yye' size='340' side='right'caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2yye' size='340' side='right'caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aquae Aquae~~]. The August 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. The August 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YYE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>~~, ~~<scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2e0b\|2e0b]], [[2zau\|2zau]], [[2zod\|2zod]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">aq_1030~~ (~~[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE]~~)~~</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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [https://pdbe.org/2yye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [https://www.ebi.ac.uk/pdbsum/2yye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yye ProSAT], [https://www.topsan.org/Proteins/RSGI/2yye 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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [https://pdbe.org/2yye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [https://www.ebi.ac.uk/pdbsum/2yye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yye ProSAT], [https://www.topsan.org/Proteins/RSGI/2yye 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: ~~Aquae~~]]	+	[[Category: Aquifex aeolicus VF5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Selenide, water dikinase]]
	[[Category: Selenocysteine Synthase]]		[[Category: Selenocysteine Synthase]]
-	[[Category: Itoh, Y]]	+	[[Category: Itoh Y]]
-	[[Category: Matsumoto, E]]	+	[[Category: Matsumoto E]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sekine S]]
-	[[Category: Sekine, S]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Full-length selenophosphate synthetase complex with atp-analog]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:42, 8 December 2021

OCA — Wed, 08 Dec 2021 10:42:41 GMT

←Older revision		Revision as of 10:42, 8 December 2021
Line 1:		Line 1:

	==Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP==		==Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP==
-	<StructureSection load='2yye' size='340' side='right' caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2yye' size='340' side='right'caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aquae Aquae]. The August 2008 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquae Aquae]. The August 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YYE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e0b\|2e0b]], [[2zau\|2zau]], [[2zod\|2zod]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e0b\|2e0b]], [[2zau\|2zau]], [[2zod\|2zod]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [~~http~~://pdbe.org/2yye PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yye PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yye ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2yye 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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [https://pdbe.org/2yye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [https://www.ebi.ac.uk/pdbsum/2yye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yye ProSAT], [https://www.topsan.org/Proteins/RSGI/2yye 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: Aquae]]		[[Category: Aquae]]
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]

OCA at 08:51, 17 October 2018

OCA — Wed, 17 Oct 2018 08:51:09 GMT

←Older revision		Revision as of 08:51, 17 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP==		==Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP==
	<StructureSection load='2yye' size='340' side='right' caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2yye' size='340' side='right' caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://pdbe.org/2yye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://www.topsan.org/Proteins/RSGI/2yye 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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://pdbe.org/2yye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yye ProSAT], [http://www.topsan.org/Proteins/RSGI/2yye 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/yy/2yye_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yy/2yye_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 02:32, 10 February 2016

OCA — Wed, 10 Feb 2016 02:32:06 GMT

←Older revision		Revision as of 02:32, 10 February 2016
Line 7:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://www.topsan.org/Proteins/RSGI/2yye 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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://pdbe.org/2yye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://www.topsan.org/Proteins/RSGI/2yye 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=2yye 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 2yye" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:10, 25 December 2014

OCA — Thu, 25 Dec 2014 11:10:17 GMT

←Older revision		Revision as of 11:10, 25 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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://www.topsan.org/Proteins/RSGI/2yye 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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://www.topsan.org/Proteins/RSGI/2yye 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 35:		Line 37:
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
	[[Category: Selenocysteine Synthase]]		[[Category: Selenocysteine Synthase]]
-	[[Category: Itoh, Y.]]	+	[[Category: Itoh, Y]]
-	[[Category: Matsumoto, E.]]	+	[[Category: Matsumoto, E]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Full-length selenophosphate synthetase complex with atp-analog]]		[[Category: Full-length selenophosphate synthetase complex with atp-analog]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:48, 10 October 2014

OCA — Fri, 10 Oct 2014 05:48:51 GMT

←Older revision		Revision as of 05:48, 10 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2yye\| PDB=2yye \| SCENE= }}~~	+	==Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP==
-	===Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP===	+	<StructureSection load='2yye' size='340' side='right' caption='[[2yye]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18773910}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YYE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e0b\|2e0b]], [[2zau\|2zau]], [[2zod\|2zod]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [http://www.ebi.ac.uk/pdbsum/2yye PDBsum], [http://www.topsan.org/Proteins/RSGI/2yye 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/yy/2yye_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>
-	~~[[2yye]] is~~ a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the ~~Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx~~.~~doi~~.~~org/10~~.~~2210~~/~~rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:018773910</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aquae]]		[[Category: Aquae]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]

OCA at 05:48, 22 January 2014

OCA — Wed, 22 Jan 2014 05:48:23 GMT

←Older revision		Revision as of 05:48, 22 January 2014
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-	[[Image:2yye.png\|left\|200px]]
-
	{{STRUCTURE_2yye\| PDB=2yye \| SCENE= }}		{{STRUCTURE_2yye\| PDB=2yye \| SCENE= }}
-
	===Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP===		===Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP===
		+	{{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==
-	[[2yye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus Aquifex aeolicus~~]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA].	+	[[2yye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE 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: Aquae]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]

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

OCA — Mon, 07 Jan 2013 17:46:51 GMT

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

←Older revision

Revision as of 17:46, 7 January 2013

OCA at 17:46, 7 January 2013

OCA — Mon, 07 Jan 2013 17:46:48 GMT

←Older revision		Revision as of 17:46, 7 January 2013
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-	{{Seed}}
	[[Image:2yye.png\|left\|200px]]		[[Image:2yye.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2yye", 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_2yye\| PDB=2yye \| SCENE= }}		{{STRUCTURE_2yye\| PDB=2yye \| SCENE= }}

	===Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP===		===Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP===

-
-	<!--
-	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==
-	~~2YYE~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA].	+	[[2yye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE 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: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
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	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 21 08:34:57 2010''

OCA at 06:34, 21 January 2010

OCA — Thu, 21 Jan 2010 06:34:59 GMT

←Older revision		Revision as of 06:34, 21 January 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2YYE is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA].	+	2YYE is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The August 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:18773910</ref><references group="xtra"/>		<ref group="xtra">PMID:18773910</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
		+	[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Selenide, water dikinase]]		[[Category: Selenide, water dikinase]]
	[[Category: Selenocysteine Synthase]]		[[Category: Selenocysteine Synthase]]
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	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 14~~:42:~~17 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 21 08:34:57 2010''