2pnq - Revision history

OCA at 09:10, 21 February 2024

2024-02-21T09:10:54Z

←Older revision		Revision as of 09:10, 21 February 2024
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	<StructureSection load='2pnq' size='340' side='right'caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='2pnq' size='340' side='right'caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.81Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Pdp1, Ppm2c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~10116 Buffalo rat])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </~~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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [https://pdbe.org/2pnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [https://www.ebi.ac.uk/pdbsum/2pnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pnq 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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [https://pdbe.org/2pnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [https://www.ebi.ac.uk/pdbsum/2pnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pnq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PDP1_RAT PDP1_RAT]] Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.	+	[https://www.uniprot.org/uniprot/PDP1_RAT PDP1_RAT] Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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=2pnq 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=2pnq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pyruvate dehydrogenase phosphatase 1 (PDP1) catalyzes dephosphorylation of pyruvate dehydrogenase (E1) in the mammalian pyruvate dehydrogenase complex (PDC), whose activity is regulated by the phosphorylation-dephosphorylation cycle by the corresponding protein kinases (PDHKs) and phosphatases. The activity of PDP1 is greatly enhanced through Ca2+ -dependent binding of the catalytic subunit (PDP1c) to the L2 (inner lipoyl) domain of dihydrolipoyl acetyltransferase (E2), which is also integrated in PDC. Here, we report the crystal structure of the rat PDP1c at 1.8 A resolution. The structure reveals that PDP1 belongs to the PPM family of protein serine/threonine phosphatases, which, in spite of a low level of sequence identity, share the structural core consisting of the central beta-sandwich flanked on both sides by loops and alpha-helices. Consistent with the previous studies, two well-fixed magnesium ions are coordinated by five active site residues and five water molecules in the PDP1c catalytic center. Structural analysis indicates that, while the central portion of the PDP1c molecule is highly conserved among the members of the PPM protein family, a number of structural insertions and deletions located at the periphery of PDP1c likely define its functional specificity towards the PDC. One notable feature of PDP1c is a long insertion (residues 98-151) forming a unique hydrophobic pocket on the surface that likely accommodates the lipoyl moiety of the E2 domain in a fashion similar to that of PDHKs. The cavity, however, appears more open than in PDHK, suggesting that its closure may be required to achieve tight, specific binding of the lipoic acid. We propose a mechanism in which the closure of the lipoic acid binding site is triggered by the formation of the intermolecular (PDP1c/L2) Ca2+ binding site in a manner reminiscent of the Ca2+ -induced closure of the regulatory domain of troponin C.
-
-	Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.,Vassylyev DG, Symersky J J Mol Biol. 2007 Jul 13;370(3):417-26. Epub 2007 May 10. PMID:17532339<ref>PMID:17532339</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2pnq" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Symersky, J~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Vassylyev, D G~~]]	+	[[Category: Symersky J]]
-	[[Category: ~~Catalytic subunit]]~~	+	[[Category: Vassylyev DG]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pdp1c]]~~	+
-	~~[[Category: Pyruvate dehydrogenase phosphatase 1~~]]	+

OCA at 15:28, 17 June 2021

2021-06-17T15:28:17Z

←Older revision		Revision as of 15:28, 17 June 2021
Line 1:		Line 1:

	==Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)==		==Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)==
-	<StructureSection load='2pnq' size='340' side='right' caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>	+	<StructureSection load='2pnq' size='340' side='right'caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [~~http~~://pdbe.org/2pnq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pnq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pnq 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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [https://pdbe.org/2pnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [https://www.ebi.ac.uk/pdbsum/2pnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pnq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PDP1_RAT PDP1_RAT]] Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.	+	[[https://www.uniprot.org/uniprot/PDP1_RAT PDP1_RAT]] Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Symersky, J]]		[[Category: Symersky, J]]
	[[Category: Vassylyev, D G]]		[[Category: Vassylyev, D G]]

OCA at 08:46, 29 August 2018

2018-08-29T08:46:03Z

←Older revision		Revision as of 08:46, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)==		==Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)==
	<StructureSection load='2pnq' size='340' side='right' caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='2pnq' size='340' side='right' caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://pdbe.org/2pnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq 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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://pdbe.org/2pnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pnq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pn/2pnq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pn/2pnq_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>
	</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=2pnq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:55, 11 September 2015

2015-09-11T07:55:36Z

←Older revision		Revision as of 07:55, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pnq' size='340' side='right' caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='2pnq' size='340' side='right' caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq 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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://pdbe.org/2pnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2pnq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Symersky, J]]		[[Category: Symersky, J]]
	[[Category: Vassylyev, D G]]		[[Category: Vassylyev, D G]]

OCA at 13:31, 25 December 2014

2014-12-25T13:31:29Z

←Older revision		Revision as of 13:31, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq 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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDP1_RAT PDP1_RAT]] Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Symersky, J.]]	+	[[Category: Symersky, J]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
	[[Category: Catalytic subunit]]		[[Category: Catalytic subunit]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Pdp1c]]		[[Category: Pdp1c]]
	[[Category: Pyruvate dehydrogenase phosphatase 1]]		[[Category: Pyruvate dehydrogenase phosphatase 1]]

OCA at 18:20, 30 September 2014

2014-09-30T18:20:05Z

←Older revision		Revision as of 18:20, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2pnq.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)==
		+	<StructureSection load='2pnq' size='340' side='right' caption='[[2pnq]], [[Resolution\|resolution]] 1.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]-phosphatase [Pyruvate dehydrogenase (acetyl-transferring)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] </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=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [http://www.ebi.ac.uk/pdbsum/2pnq 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/pn/2pnq_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 ==
		+	Pyruvate dehydrogenase phosphatase 1 (PDP1) catalyzes dephosphorylation of pyruvate dehydrogenase (E1) in the mammalian pyruvate dehydrogenase complex (PDC), whose activity is regulated by the phosphorylation-dephosphorylation cycle by the corresponding protein kinases (PDHKs) and phosphatases. The activity of PDP1 is greatly enhanced through Ca2+ -dependent binding of the catalytic subunit (PDP1c) to the L2 (inner lipoyl) domain of dihydrolipoyl acetyltransferase (E2), which is also integrated in PDC. Here, we report the crystal structure of the rat PDP1c at 1.8 A resolution. The structure reveals that PDP1 belongs to the PPM family of protein serine/threonine phosphatases, which, in spite of a low level of sequence identity, share the structural core consisting of the central beta-sandwich flanked on both sides by loops and alpha-helices. Consistent with the previous studies, two well-fixed magnesium ions are coordinated by five active site residues and five water molecules in the PDP1c catalytic center. Structural analysis indicates that, while the central portion of the PDP1c molecule is highly conserved among the members of the PPM protein family, a number of structural insertions and deletions located at the periphery of PDP1c likely define its functional specificity towards the PDC. One notable feature of PDP1c is a long insertion (residues 98-151) forming a unique hydrophobic pocket on the surface that likely accommodates the lipoyl moiety of the E2 domain in a fashion similar to that of PDHKs. The cavity, however, appears more open than in PDHK, suggesting that its closure may be required to achieve tight, specific binding of the lipoic acid. We propose a mechanism in which the closure of the lipoic acid binding site is triggered by the formation of the intermolecular (PDP1c/L2) Ca2+ binding site in a manner reminiscent of the Ca2+ -induced closure of the regulatory domain of troponin C.

-	~~{{STRUCTURE_2pnq\| PDB=2pnq \| SCENE= }}~~	+	Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.,Vassylyev DG, Symersky J J Mol Biol. 2007 Jul 13;370(3):417-26. Epub 2007 May 10. PMID:17532339<ref>PMID:17532339</ref>

-	~~===Crystal structure~~ of ~~pyruvate dehydrogenase phosphatase 1 (PDP1)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17532339}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2pnq]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017532339<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Symersky, J.]]		[[Category: Symersky, J.]]

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

2013-01-07T13:11:34Z

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

←Older revision

Revision as of 13:11, 7 January 2013

OCA at 13:11, 7 January 2013

2013-01-07T13:11:31Z

←Older revision		Revision as of 13:11, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2pnq.png\|left\|200px]]		[[Image:2pnq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pnq", 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_2pnq\| PDB=2pnq \| SCENE= }}		{{STRUCTURE_2pnq\| PDB=2pnq \| SCENE= }}

	===Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)===		===Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17532339}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17532339 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17532339}}		{{ABSTRACT_PUBMED_17532339}}

	==About this Structure==		==About this Structure==
-	~~2PNQ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA].	+	[[2pnq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17532339~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017532339</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Symersky, J.]]		[[Category: Symersky, J.]]
	[[Category: Vassylyev, D G.]]		[[Category: Vassylyev, D G.]]
	[[Category: Catalytic subunit]]		[[Category: Catalytic subunit]]
-	[[Category: Crystal structure]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Pdp1c]]		[[Category: Pdp1c]]
	[[Category: Pyruvate dehydrogenase phosphatase 1]]		[[Category: Pyruvate dehydrogenase phosphatase 1]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:28:41 2009''

OCA at 15:28, 17 February 2009

2009-02-17T15:28:43Z

←Older revision		Revision as of 15:28, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2PNQ is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA].	+	2PNQ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA].

	==Reference==		==Reference==
-	~~Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications., Vassylyev DG, Symersky J, J Mol Biol. 2007 Jul 13;370(3):417-26. Epub 2007 May 10.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17532339 17532339]~~	+	<ref group="xtra">PMID:17532339</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Single protein]]
	[[Category: Symersky, J.]]		[[Category: Symersky, J.]]
	[[Category: Vassylyev, D G.]]		[[Category: Vassylyev, D G.]]
Line 34:		Line 33:
	[[Category: Pyruvate dehydrogenase phosphatase 1]]		[[Category: Pyruvate dehydrogenase phosphatase 1]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:27:~~27 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:28:41 2009''

OCA at 21:27, 28 July 2008

2008-07-28T21:27:34Z

←Older revision		Revision as of 21:27, 28 July 2008
Line 1:		Line 1:
-	[[Image:2pnq.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2pnq.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2pnq\| PDB=2pnq \| SCENE= }}		{{STRUCTURE_2pnq\| PDB=2pnq \| SCENE= }}

-	~~'''~~Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)~~'''~~	+	===Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)===


-	~~==Overview==~~	+	<!--
-	~~Pyruvate dehydrogenase phosphatase 1 (PDP1) catalyzes dephosphorylation of pyruvate dehydrogenase (E1) in the mammalian pyruvate dehydrogenase complex (PDC)~~, ~~whose activity is regulated by~~ the phosphorylation-dephosphorylation cycle by the corresponding protein kinases (PDHKs) and phosphatases. The activity of PDP1 is greatly enhanced through Ca2+ -dependent binding of the catalytic subunit (PDP1c) to the L2 (~~inner lipoyl) domain of dihydrolipoyl acetyltransferase (E2), which is also integrated in PDC. Here, we report the crystal structure of the rat PDP1c~~ at ~~1.8 A resolution. The structure reveals that PDP1 belongs to the PPM family of protein serine~~/~~threonine phosphatases, which, in spite of a low level of sequence identity, share the structural core consisting of the central beta-sandwich flanked on both sides by loops and alpha-helices~~. ~~Consistent with the previous studies, two well-fixed magnesium ions are coordinated by five active site residues and five water molecules in the PDP1c catalytic center~~. ~~Structural analysis indicates that~~, ~~while the central portion of the PDP1c molecule~~ is ~~highly conserved among~~ the ~~members of the PPM protein family, a~~ number ~~of structural insertions and deletions located at the periphery of PDP1c likely define its functional specificity towards the PDC~~. ~~One notable feature of PDP1c is a long insertion (residues 98~~-151) forming a unique hydrophobic pocket on the surface that likely accommodates the lipoyl moiety of the E2 domain in a fashion similar to that of PDHKs. The cavity, however, appears more open than in PDHK, suggesting that its closure may be required to achieve tight, specific binding of the lipoic acid. We propose a mechanism in which the closure of the lipoic acid binding site is triggered by the formation of the intermolecular (PDP1c/L2) Ca2+ binding site in a manner reminiscent of the Ca2+ -~~induced closure of the regulatory domain of troponin C.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17532339}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17532339 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17532339}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Pdp1c]]		[[Category: Pdp1c]]
	[[Category: Pyruvate dehydrogenase phosphatase 1]]		[[Category: Pyruvate dehydrogenase phosphatase 1]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 13:~~29:44 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 00:27:27 2008''