2ik1 - Revision history

OCA at 10:12, 30 August 2023

OCA — Wed, 30 Aug 2023 10:12:41 GMT

←Older revision		Revision as of 10:12, 30 August 2023
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	<StructureSection load='2ik1' size='340' side='right'caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2ik1' size='340' side='right'caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MES:2~~-~~(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>IPP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4932 ATCC 18824])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1]~~ </~~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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [https://pdbe.org/2ik1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [https://www.ebi.ac.uk/pdbsum/2ik1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik1 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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [https://pdbe.org/2ik1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [https://www.ebi.ac.uk/pdbsum/2ik1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IPYR_YEAST IPYR_YEAST]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
-	[[Category: Inorganic diphosphatase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ahonen~~, A K~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Goldman, A]]	+	[[Category: Ahonen AK]]
-	[[Category: Heikinheimo, P]]	+	[[Category: Goldman A]]
-	[[Category: Lahti, R]]	+	[[Category: Heikinheimo P]]
-	[[Category: Oksanen, E]]	+	[[Category: Lahti R]]
-	[[Category: Tuominen, H]]	+	[[Category: Oksanen E]]
-	[[Category: Tuominen, V]]	+	[[Category: Tuominen H]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Tuominen V]]
-	~~[[Category: Inorganic pyrophosphatase]]~~	+
-	~~[[Category: Mutagenesis]]~~	+
-	~~[[Category: Structure-function~~]]	+

OCA at 11:17, 31 March 2021

OCA — Wed, 31 Mar 2021 11:17:39 GMT

←Older revision		Revision as of 11:17, 31 March 2021
Line 1:		Line 1:

	==Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate==		==Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate==
-	<StructureSection load='2ik1' size='340' side='right' caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='2ik1' size='340' side='right'caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [~~http~~://pdbe.org/2ik1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ik1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik1 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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [https://pdbe.org/2ik1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [https://www.ebi.ac.uk/pdbsum/2ik1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]	+	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Ahonen, A K]]		[[Category: Ahonen, A K]]
	[[Category: Goldman, A]]		[[Category: Goldman, A]]

OCA at 08:25, 4 July 2018

OCA — Wed, 04 Jul 2018 08:25:38 GMT

←Older revision		Revision as of 08:25, 4 July 2018
Line 1:		Line 1:
		+
	==Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate==		==Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate==
	<StructureSection load='2ik1' size='340' side='right' caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2ik1' size='340' side='right' caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://pdbe.org/2ik1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://pdbe.org/2ik1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/2ik1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/2ik1_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 20:34, 8 February 2016

OCA — Mon, 08 Feb 2016 20:34:21 GMT

←Older revision		Revision as of 20:34, 8 February 2016
Line 17:		Line 17:
	<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=2ik1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:10, 10 September 2015

OCA — Thu, 10 Sep 2015 15:10:13 GMT

←Older revision		Revision as of 15:10, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2ik1' size='340' side='right' caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2ik1' size='340' side='right' caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://pdbe.org/2ik1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2ik1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Ahonen, A K]]		[[Category: Ahonen, A K]]
	[[Category: Goldman, A]]		[[Category: Goldman, A]]

OCA at 08:30, 16 January 2015

OCA — Fri, 16 Jan 2015 08:30:18 GMT

←Older revision		Revision as of 08:30, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Ahonen, A K.]]	+	[[Category: Ahonen, A K]]
-	[[Category: Goldman, A.]]	+	[[Category: Goldman, A]]
-	[[Category: Heikinheimo, P.]]	+	[[Category: Heikinheimo, P]]
-	[[Category: Lahti, R.]]	+	[[Category: Lahti, R]]
-	[[Category: Oksanen, E.]]	+	[[Category: Oksanen, E]]
-	[[Category: Tuominen, H.]]	+	[[Category: Tuominen, H]]
-	[[Category: Tuominen, V.]]	+	[[Category: Tuominen, V]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Inorganic pyrophosphatase]]		[[Category: Inorganic pyrophosphatase]]
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]
	[[Category: Structure-function]]		[[Category: Structure-function]]

OCA at 05:51, 29 September 2014

OCA — Mon, 29 Sep 2014 05:51:09 GMT

←Older revision		Revision as of 05:51, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2ik1.~~png~~\|~~left~~\|200px]]	+	==Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate==
		+	<StructureSection load='2ik1' size='340' side='right' caption='[[2ik1]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ik1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IK1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wgi\|1wgi]], [[1e9g\|1e9g]], [[1e6a\|1e6a]], [[2ihp\|2ihp]], [[2ik0\|2ik0]], [[2ik2\|2ik2]], [[2ik4\|2ik4]], [[2ik6\|2ik6]], [[2ik7\|2ik7]], [[2ik9\|2ik9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></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=2ik1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ik1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ik1 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/ik/2ik1_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 ==
		+	We have determined the structures of the wild type and seven active site variants of yeast inorganic pyrophosphatase (PPase) in the presence of Mg2+ and phosphate, providing the first complete structural description of its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and require four divalent metal cations for catalysis; magnesium provides the highest activity. The crystal form chosen contains two monomers in the asymmetric unit, corresponding to distinct catalytic intermediates. In the "closed" wild-type active site, one of the two product phosphates has already dissociated, while the D115E variant "open" conformation is of the hitherto unobserved two-phosphate and two-"bridging" water active site. The mutations affect metal binding and the hydrogen bonding network in the active site, allowing us to explain the effects of mutations. For instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the absence of substrate, preserving hydrogen bonding in the active site and leading to relatively small changes in solution properties. This is not true in the presence of substrate, when F93 is forced back into the active site. Such subtle changes underline how low the energy barriers are between thermodynamically favorable conformations of the enzyme. The structures also allow us to associate metal binding constants to specific sites. Finally, the wild type and the D152E variant contain a phosphate ion adjacent to the active site, showing for the first time how product is released through a channel of flexible cationic side chains.

-	~~{{STRUCTURE_2ik1\| PDB=2ik1 \| SCENE= }}~~	+	A complete structural description of the catalytic cycle of yeast pyrophosphatase.,Oksanen E, Ahonen AK, Tuominen H, Tuominen V, Lahti R, Goldman A, Heikinheimo P Biochemistry. 2007 Feb 6;46(5):1228-39. PMID:17260952<ref>PMID:17260952</ref>

-	~~===Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17260952}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2ik1]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA].~~	+

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]		*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017260952<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 11:23, 20 October 2012

OCA — Sat, 20 Oct 2012 11:23:47 GMT

←Older revision		Revision as of 11:23, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2ik1]] is a 2 chain structure ~~of [[Inorganic pyrophosphatase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA].	+	[[2ik1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA].

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

OCA: Protected "2ik1" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 05:13:24 GMT

Protected "2ik1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:13, 26 July 2012

OCA at 05:13, 26 July 2012

OCA — Thu, 26 Jul 2012 05:13:21 GMT

←Older revision		Revision as of 05:13, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ik1.png\|left\|200px]]		[[Image:2ik1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ik1", 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_2ik1\| PDB=2ik1 \| SCENE= }}		{{STRUCTURE_2ik1\| PDB=2ik1 \| SCENE= }}

	===Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate===		===Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17260952}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17260952 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17260952}}		{{ABSTRACT_PUBMED_17260952}}

	==About this Structure==		==About this Structure==
-	~~2IK1~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA].	+	[[2ik1]] is a 2 chain structure of [[Inorganic pyrophosphatase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK1 OCA].
		+
		+	==See Also==
		+	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17260952~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017260952</ref><references group="xtra"/>
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 33:		Line 24:
	[[Category: Tuominen, H.]]		[[Category: Tuominen, H.]]
	[[Category: Tuominen, V.]]		[[Category: Tuominen, V.]]
		+	[[Category: Hydrolase]]
	[[Category: Inorganic pyrophosphatase]]		[[Category: Inorganic pyrophosphatase]]
-	[[Category: Mechanism]]
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]
	[[Category: Structure-function]]		[[Category: Structure-function]]
-	[[Category: X-ray crystallography]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:54:25 2009''