1wgj - Revision history

OCA at 08:47, 14 February 2024

OCA — Wed, 14 Feb 2024 08:47:47 GMT

←Older revision		Revision as of 08:47, 14 February 2024
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	<StructureSection load='1wgj' size='340' side='right'caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1wgj' size='340' side='right'caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PPA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4932 ATCC 18824])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [https://pdbe.org/1wgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [https://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wgj ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [~~http~~://pdbe.org/1wgj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wgj 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]]
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	</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=1wgj 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=1wgj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Soluble inorganic pyrophosphatase (PPase), an essential enzyme central to phosphorus metabolism, catalyzes the hydrolysis of the phosphoanhydride bond in inorganic pyrophosphate. Catalysis requires divalent metal ions which affect the apparent pKas of the essential general acid and base on the enzyme, and the pKa of the substrate. Three to five metal ions are required for maximal activity, depending on pH and enzyme source. A detailed understanding of catalysis would aid both in understanding the nature of biological mechanisms of phosphoryl transfer, and in understanding the role of divalent cations. Without a high-resolution complex structure such a model has previously been unobtainable. RESULTS: We report the first two high-resolution structures of yeast PPase, at 2.2 and 2.0 A resolution with R factors of around 17%. One structure contains the two activating metal ions; the other, the product (MnPi)2 as well. The latter structure shows an extensive network of hydrogen bond and metal ion interactions that account for virtually every lone pair on the product phosphates. It also contains a water molecule/hydroxide ion bridging two metal ions and, uniquely, a phosphate bound to four Mn2+ ions. CONCLUSIONS: Our structure-based model of the PPase mechanism posits that the nucleophile is the hydroxide ion mentioned above. This aspect of the mechanism is formally analogous to the "two-metal ion' mechanism of alkaline phosphatase, exonucleases and polymerases. A third metal ion coordinates another water molecule that is probably the required general acid. Extensive Lewis acid coordination and hydrogen bonds provide charge shielding of the electrophile and lower the pKa of the leaving group. This "three-metal ion' mechanism is in detail different from that of other phosphoryl transfer enzymes, presumably reflecting how ancient the reaction is.
-
-	The structural basis for pyrophosphatase catalysis.,Heikinheimo P, Lehtonen J, Baykov A, Lahti R, Cooperman BS, Goldman A Structure. 1996 Dec 15;4(12):1491-508. PMID:8994974<ref>PMID:8994974</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wgj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]		*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
-	[[Category: Inorganic diphosphatase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Goldman, A~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Heikinheimo, P~~]]	+	[[Category: Goldman A]]
-	[[Category: ~~Lehtonen, J~~]]	+	[[Category: Heikinheimo P]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Lehtonen J]]
-	~~[[Category: Manganese]]~~	+
-	~~[[Category: Pyrophosphate phosphohydrolase~~]]	+

OCA at 07:45, 30 December 2020

OCA — Wed, 30 Dec 2020 07:45:12 GMT

←Older revision		Revision as of 07:45, 30 December 2020
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	==STRUCTURE OF INORGANIC PYROPHOSPHATASE==		==STRUCTURE OF INORGANIC PYROPHOSPHATASE==
-	<StructureSection load='1wgj' size='340' side='right' caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1wgj' size='340' side='right'caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=MN:MANGANESE+(II)+ION'>MN</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">PPA1 ([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">PPA1 ([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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://pdbe.org/1wgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wgj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://pdbe.org/1wgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wgj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]	+	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Goldman, A]]		[[Category: Goldman, A]]
	[[Category: Heikinheimo, P]]		[[Category: Heikinheimo, P]]

OCA at 16:33, 11 April 2018

OCA — Wed, 11 Apr 2018 16:33:16 GMT

←Older revision		Revision as of 16:33, 11 April 2018
Line 1:		Line 1:
		+
	==STRUCTURE OF INORGANIC PYROPHOSPHATASE==		==STRUCTURE OF INORGANIC PYROPHOSPHATASE==
	<StructureSection load='1wgj' size='340' side='right' caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1wgj' size='340' side='right' caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPA1 ([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">PPA1 ([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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://pdbe.org/1wgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj 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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://pdbe.org/1wgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wgj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wg/1wgj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wg/1wgj_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 15:22, 8 February 2016

OCA — Mon, 08 Feb 2016 15:22:33 GMT

←Older revision		Revision as of 15:22, 8 February 2016
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	<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=1wgj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:54, 10 September 2015

OCA — Thu, 10 Sep 2015 12:54:53 GMT

←Older revision		Revision as of 12:54, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1wgj' size='340' side='right' caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1wgj' size='340' side='right' caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">PPA1 ([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">PPA1 ([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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj 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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://pdbe.org/1wgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1wgj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Goldman, A]]		[[Category: Goldman, A]]
	[[Category: Heikinheimo, P]]		[[Category: Heikinheimo, P]]

OCA at 13:53, 6 January 2015

OCA — Tue, 06 Jan 2015 13:53:21 GMT

←Older revision		Revision as of 13:53, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPA1 ([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">PPA1 ([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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj 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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj 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 35:		Line 35:
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Goldman, A.]]	+	[[Category: Goldman, A]]
-	[[Category: Heikinheimo, P.]]	+	[[Category: Heikinheimo, P]]
-	[[Category: Lehtonen, J.]]	+	[[Category: Lehtonen, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Manganese]]		[[Category: Manganese]]
	[[Category: Pyrophosphate phosphohydrolase]]		[[Category: Pyrophosphate phosphohydrolase]]

OCA at 21:59, 28 September 2014

OCA — Sun, 28 Sep 2014 21:59:48 GMT

←Older revision		Revision as of 21:59, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wgj.~~png~~\|~~left~~\|200px]]	+	==STRUCTURE OF INORGANIC PYROPHOSPHATASE==
		+	<StructureSection load='1wgj' size='340' side='right' caption='[[1wgj]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WGJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPA1 ([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=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [http://www.ebi.ac.uk/pdbsum/1wgj 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/wg/1wgj_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 ==
		+	BACKGROUND: Soluble inorganic pyrophosphatase (PPase), an essential enzyme central to phosphorus metabolism, catalyzes the hydrolysis of the phosphoanhydride bond in inorganic pyrophosphate. Catalysis requires divalent metal ions which affect the apparent pKas of the essential general acid and base on the enzyme, and the pKa of the substrate. Three to five metal ions are required for maximal activity, depending on pH and enzyme source. A detailed understanding of catalysis would aid both in understanding the nature of biological mechanisms of phosphoryl transfer, and in understanding the role of divalent cations. Without a high-resolution complex structure such a model has previously been unobtainable. RESULTS: We report the first two high-resolution structures of yeast PPase, at 2.2 and 2.0 A resolution with R factors of around 17%. One structure contains the two activating metal ions; the other, the product (MnPi)2 as well. The latter structure shows an extensive network of hydrogen bond and metal ion interactions that account for virtually every lone pair on the product phosphates. It also contains a water molecule/hydroxide ion bridging two metal ions and, uniquely, a phosphate bound to four Mn2+ ions. CONCLUSIONS: Our structure-based model of the PPase mechanism posits that the nucleophile is the hydroxide ion mentioned above. This aspect of the mechanism is formally analogous to the "two-metal ion' mechanism of alkaline phosphatase, exonucleases and polymerases. A third metal ion coordinates another water molecule that is probably the required general acid. Extensive Lewis acid coordination and hydrogen bonds provide charge shielding of the electrophile and lower the pKa of the leaving group. This "three-metal ion' mechanism is in detail different from that of other phosphoryl transfer enzymes, presumably reflecting how ancient the reaction is.

-	~~{{STRUCTURE_1wgj\| PDB=1wgj \| SCENE= }}~~	+	The structural basis for pyrophosphatase catalysis.,Heikinheimo P, Lehtonen J, Baykov A, Lahti R, Cooperman BS, Goldman A Structure. 1996 Dec 15;4(12):1491-508. PMID:8994974<ref>PMID:8994974</ref>

-	~~===STRUCTURE OF INORGANIC PYROPHOSPHATASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8994974}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1wgj]] 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=1WGJ OCA].~~	+

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]		*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008994974<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 10:35, 20 October 2012

OCA — Sat, 20 Oct 2012 10:35:34 GMT

←Older revision		Revision as of 10:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1wgj]] 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=1WGJ OCA].	+	[[1wgj]] 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=1WGJ OCA].

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

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

OCA — Thu, 26 Jul 2012 02:37:47 GMT

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

←Older revision

Revision as of 02:37, 26 July 2012

OCA at 02:37, 26 July 2012

OCA — Thu, 26 Jul 2012 02:37:45 GMT

←Older revision		Revision as of 02:37, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wgj.png\|left\|200px]]		[[Image:1wgj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wgj", 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_1wgj\| PDB=1wgj \| SCENE= }}		{{STRUCTURE_1wgj\| PDB=1wgj \| SCENE= }}

	===STRUCTURE OF INORGANIC PYROPHOSPHATASE===		===STRUCTURE OF INORGANIC PYROPHOSPHATASE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8994974}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8994974 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8994974}}		{{ABSTRACT_PUBMED_8994974}}

	==About this Structure==		==About this Structure==
-	~~1WGJ~~ 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=1WGJ OCA].	+	[[1wgj]] 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=1WGJ OCA].
		+
		+	==See Also==
		+	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8994974~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008994974</ref><references group="xtra"/>
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 32:		Line 23:
	[[Category: Manganese]]		[[Category: Manganese]]
	[[Category: Pyrophosphate phosphohydrolase]]		[[Category: Pyrophosphate phosphohydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:59:15 2009''