1e6a - Revision history

OCA at 08:47, 9 May 2024

2024-05-09T08:47:08Z

←Older revision		Revision as of 08:47, 9 May 2024
Line 20:		Line 20:
	</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=1e6a 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=1e6a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The wealth of kinetic and structural information makes inorganic pyrophosphatases (PPases) a good model system to study the details of enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed phosphoryl transfer 10(10)-fold: but how? Our structures of the yeast PPase product complex at 1.15 A and fluoride-inhibited complex at 1.9 A visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps around chemical catalysis and provide strong evidence that a water molecule (O(nu)) directly attacks PPi with a pK(a) vastly lowered by coordination to two metal ions and D117. They also suggest that a low-barrier hydrogen bond (LBHB) forms between D117 and O(nu), in part because of steric crowding by W100 and N116. Direct visualization of the double bonds on the phosphates appears possible. The flexible side chains at the top of the active site absorb the motion involved in the reaction, which may help accelerate catalysis. Relaxation of the product allows a new nucleophile to be generated and creates symmetry in the elementary catalytic steps on the enzyme. We are thus moving closer to understanding phosphoryl transfer in PPases at the quantum mechanical level. Ultra-high resolution structures can thus tease out overlapping complexes and so are as relevant to discussion of enzyme mechanism as structures produced by time-resolved crystallography.
		+
		+	Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase.,Heikinheimo P, Tuominen V, Ahonen AK, Teplyakov A, Cooperman BS, Baykov AA, Lahti R, Goldman A Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3121-6. Epub 2001 Mar 6. PMID:11248042<ref>PMID:11248042</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1e6a" 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>

OCA at 09:59, 20 March 2024

2024-03-20T09:59:13Z

←Older revision		Revision as of 09:59, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='1e6a' size='340' side='right'caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e6a' size='340' side='right'caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 1.9Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPA1 ([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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [https://pdbe.org/1e6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [https://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a 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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [https://pdbe.org/1e6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [https://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a 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 20:		Line 20:
	</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=1e6a 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=1e6a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The wealth of kinetic and structural information makes inorganic pyrophosphatases (PPases) a good model system to study the details of enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed phosphoryl transfer 10(10)-fold: but how? Our structures of the yeast PPase product complex at 1.15 A and fluoride-inhibited complex at 1.9 A visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps around chemical catalysis and provide strong evidence that a water molecule (O(nu)) directly attacks PPi with a pK(a) vastly lowered by coordination to two metal ions and D117. They also suggest that a low-barrier hydrogen bond (LBHB) forms between D117 and O(nu), in part because of steric crowding by W100 and N116. Direct visualization of the double bonds on the phosphates appears possible. The flexible side chains at the top of the active site absorb the motion involved in the reaction, which may help accelerate catalysis. Relaxation of the product allows a new nucleophile to be generated and creates symmetry in the elementary catalytic steps on the enzyme. We are thus moving closer to understanding phosphoryl transfer in PPases at the quantum mechanical level. Ultra-high resolution structures can thus tease out overlapping complexes and so are as relevant to discussion of enzyme mechanism as structures produced by time-resolved crystallography.
-
-	Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase.,Heikinheimo P, Tuominen V, Ahonen AK, Teplyakov A, Cooperman BS, Baykov AA, Lahti R, Goldman A Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3121-6. Epub 2001 Mar 6. PMID:11248042<ref>PMID:11248042</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1e6a" 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: Ahonen, A K]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Baykov~~, A A~~]]	+	[[Category: Ahonen A-K]]
-	[[Category: Cooperman~~, B S~~]]	+	[[Category: Baykov AA]]
-	[[Category: Goldman, A]]	+	[[Category: Cooperman BS]]
-	[[Category: Heikinheimo, P]]	+	[[Category: Goldman A]]
-	[[Category: Lahti, R]]	+	[[Category: Heikinheimo P]]
-	[[Category: Teplyakov, A]]	+	[[Category: Lahti R]]
-	[[Category: Tuominen, V]]	+	[[Category: Teplyakov A]]
-	~~[[Category: Hydrolysis]]~~	+	[[Category: Tuominen V]]
-	~~[[Category: Phosphoryl transfer~~]]	+

OCA at 05:45, 28 April 2021

2021-04-28T05:45:37Z

←Older revision		Revision as of 05:45, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='1e6a' size='340' side='right'caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e6a' size='340' side='right'caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1E6A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</div></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 ([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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [~~http~~://pdbe.org/1e6a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a 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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [https://pdbe.org/1e6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [https://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a 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/>

OCA at 11:31, 10 May 2019

2019-05-10T11:31:31Z

←Older revision		Revision as of 11:31, 10 May 2019
Line 1:		Line 1:

	==Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase==		==Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase==
-	<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1e6a' size='340' side='right'caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
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: Baykov, A A]]		[[Category: Baykov, A A]]

OCA at 07:00, 12 December 2018

2018-12-12T07:00:50Z

←Older revision		Revision as of 07:00, 12 December 2018
Line 3:		Line 3:
	<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e6a]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://pdbe.org/1e6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a ProSAT]</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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://pdbe.org/1e6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a ProSAT]</span></td></tr>
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/e6/1e6a_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/1e6a_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>
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Ahonen, A K]]		[[Category: Ahonen, A K]]

OCA at 03:45, 6 September 2017

2017-09-06T03:45:38Z

←Older revision		Revision as of 03:45, 6 September 2017
Line 1:		Line 1:
-	==~~FLUORIDE~~-~~INHIBITED SUBSTRATE COMPLEX OF SACCHAROMYCES CEREVISIAE INORGANIC PYROPHOSPHATASE~~==	+
		+	==Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase==
	<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e6a]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://pdbe.org/1e6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a 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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://pdbe.org/1e6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6a ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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=1e6a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Ahonen, A K]]		[[Category: Ahonen, A K]]

OCA at 01:13, 12 September 2015

2015-09-12T01:13:30Z

←Older revision		Revision as of 01:13, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a 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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://pdbe.org/1e6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a 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 1e6a" 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: Baykov, A A]]		[[Category: Baykov, A A]]

OCA at 23:21, 22 December 2014

2014-12-22T23:21:00Z

←Older revision		Revision as of 23:21, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a 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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a 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: Baykov, A A.]]	+	[[Category: Baykov, A A]]
-	[[Category: Cooperman, B S.]]	+	[[Category: Cooperman, B S]]
-	[[Category: Goldman, A.]]	+	[[Category: Goldman, A]]
-	[[Category: Heikinheimo, P.]]	+	[[Category: Heikinheimo, P]]
-	[[Category: Lahti, R.]]	+	[[Category: Lahti, R]]
-	[[Category: Teplyakov, A.]]	+	[[Category: Teplyakov, A]]
-	[[Category: Tuominen, V.]]	+	[[Category: Tuominen, V]]
	[[Category: Hydrolysis]]		[[Category: Hydrolysis]]
	[[Category: Phosphoryl transfer]]		[[Category: Phosphoryl transfer]]

OCA at 10:34, 10 September 2014

2014-09-10T10:34:08Z

←Older revision		Revision as of 10:34, 10 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1e6a.~~png~~\|~~left~~\|200px]]	+	==FLUORIDE-INHIBITED SUBSTRATE COMPLEX OF SACCHAROMYCES CEREVISIAE INORGANIC PYROPHOSPHATASE==
		+	<StructureSection load='1e6a' size='340' side='right' caption='[[1e6a]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1e6a]] 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=1E6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6A FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ypp\|1ypp]], [[1wgj\|1wgj]], [[1wgi\|1wgi]], [[1huj\|1huj]], [[1huk\|1huk]], [[117e\|117e]], [[8prk\|8prk]]</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><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=1e6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e6a RCSB], [http://www.ebi.ac.uk/pdbsum/1e6a 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/e6/1e6a_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 ==
		+	The wealth of kinetic and structural information makes inorganic pyrophosphatases (PPases) a good model system to study the details of enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed phosphoryl transfer 10(10)-fold: but how? Our structures of the yeast PPase product complex at 1.15 A and fluoride-inhibited complex at 1.9 A visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps around chemical catalysis and provide strong evidence that a water molecule (O(nu)) directly attacks PPi with a pK(a) vastly lowered by coordination to two metal ions and D117. They also suggest that a low-barrier hydrogen bond (LBHB) forms between D117 and O(nu), in part because of steric crowding by W100 and N116. Direct visualization of the double bonds on the phosphates appears possible. The flexible side chains at the top of the active site absorb the motion involved in the reaction, which may help accelerate catalysis. Relaxation of the product allows a new nucleophile to be generated and creates symmetry in the elementary catalytic steps on the enzyme. We are thus moving closer to understanding phosphoryl transfer in PPases at the quantum mechanical level. Ultra-high resolution structures can thus tease out overlapping complexes and so are as relevant to discussion of enzyme mechanism as structures produced by time-resolved crystallography.

-	~~{{STRUCTURE_1e6a\| PDB=1e6a \| SCENE= }}~~	+	Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase.,Heikinheimo P, Tuominen V, Ahonen AK, Teplyakov A, Cooperman BS, Baykov AA, Lahti R, Goldman A Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3121-6. Epub 2001 Mar 6. PMID:11248042<ref>PMID:11248042</ref>

-	~~===FLUORIDE-INHIBITED SUBSTRATE COMPLEX OF SACCHAROMYCES CEREVISIAE INORGANIC PYROPHOSPHATASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11248042}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1e6a]] 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=1E6A OCA].~~	+

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]		*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011248042<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 22:04, 20 October 2012

2012-10-20T22:04:42Z

←Older revision		Revision as of 22:04, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[1e6a]] 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=1E6A OCA].	+	[[1e6a]] 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=1E6A OCA].

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