1y9i - Revision history

OCA at 08:01, 15 May 2024

OCA — Wed, 15 May 2024 08:01:34 GMT

←Older revision		Revision as of 08:01, 15 May 2024
Line 1:		Line 1:

	==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==		==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==
-	<StructureSection load='1y9i' size='340' side='right'caption='[[1y9i]]' scene=''>	+	<StructureSection load='1y9i' size='340' side='right'caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>
-	</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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [https://pdbe.org/1y9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [https://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y9i ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [https://pdbe.org/1y9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [https://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y9i ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8Y4N7_LISMO Q8Y4N7_LISMO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		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=1y9i 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=1y9i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphatidylglycerophosphatase (PGPase), an enzyme involved in lipid metabolism, catalyzes formation of phosphatidylglycerol from phosphatidylglycerophosphate. Phosphatidylglycerol is a multifunctional phospholipid, found in the biological membranes of many organisms. Here, we report the crystal structure of Listeria monocytogenes PGPase at 1.8 A resolution. PGPase, an all-helical molecule, forms a homotetramer. Each protomer contains an independent active site with two metal ions, Ca(2+) and Mg(2+), forming a hetero-binuclear center located in a hydrophilic cavity near the surface of the molecule. The binuclear center, conserved ligands, metal-bound water molecules, and an Asp-His dyad form the active site. The catalytic mechanism of this enzyme is likely to proceed via binuclear metal activated nucleophilic water. The binuclear metal-binding active-site environment of this structure should provide insights into substrate binding and metal-dependent catalysis. A long channel with inter-linked linear water chains, termed "proton wires," is observed at the tetramer interface. Comparison of similar water chain structures in photosynthetic reaction centers (RCs), Cytochrome f, gramicidin, and bacteriorhodopsin, suggests that PGPase may conduct protons via proton wires.
		+
		+	Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires".,Kumaran D, Bonanno JB, Burley SK, Swaminathan S Proteins. 2006 Sep 1;64(4):851-62. PMID:16838328<ref>PMID:16838328</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1y9i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Listeria monocytogenes]]
	[[Category: Burley SK]]		[[Category: Burley SK]]
	[[Category: Kumaran D]]		[[Category: Kumaran D]]
	[[Category: Swaminathan S]]		[[Category: Swaminathan S]]

OCA at 09:07, 21 April 2021

OCA — Wed, 21 Apr 2021 09:07:21 GMT

←Older revision		Revision as of 09:07, 21 April 2021
Line 1:		Line 1:

	==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==		==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==
-	<StructureSection load='1y9i' size='340' side='right'caption='[[1y9i]]~~, [[Resolution\|resolution]] 1.80Å~~' scene=''>	+	<StructureSection load='1y9i' size='340' side='right'caption='[[1y9i]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [https://pdbe.org/1y9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [https://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y9i ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [~~http~~://pdbe.org/1y9i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y9i ProSAT], [~~http~~://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 18:		Line 16:
	</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=1y9i 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=1y9i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phosphatidylglycerophosphatase (PGPase), an enzyme involved in lipid metabolism, catalyzes formation of phosphatidylglycerol from phosphatidylglycerophosphate. Phosphatidylglycerol is a multifunctional phospholipid, found in the biological membranes of many organisms. Here, we report the crystal structure of Listeria monocytogenes PGPase at 1.8 A resolution. PGPase, an all-helical molecule, forms a homotetramer. Each protomer contains an independent active site with two metal ions, Ca(2+) and Mg(2+), forming a hetero-binuclear center located in a hydrophilic cavity near the surface of the molecule. The binuclear center, conserved ligands, metal-bound water molecules, and an Asp-His dyad form the active site. The catalytic mechanism of this enzyme is likely to proceed via binuclear metal activated nucleophilic water. The binuclear metal-binding active-site environment of this structure should provide insights into substrate binding and metal-dependent catalysis. A long channel with inter-linked linear water chains, termed "proton wires," is observed at the tetramer interface. Comparison of similar water chain structures in photosynthetic reaction centers (RCs), Cytochrome f, gramicidin, and bacteriorhodopsin, suggests that PGPase may conduct protons via proton wires.
-
-	Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires".,Kumaran D, Bonanno JB, Burley SK, Swaminathan S Proteins. 2006 Sep 1;64(4):851-62. PMID:16838328<ref>PMID:16838328</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1y9i" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Burley~~, S K~~]]	+	[[Category: Burley SK]]
-	[[Category: Kumaran, D]]	+	[[Category: Kumaran D]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Swaminathan S]]
-	[[Category: Swaminathan, S]]	+
-	~~[[Category: Helical bundle]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Putative pgpa]]~~	+
-	~~[[Category: Tetramer]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 13:44, 17 July 2019

OCA — Wed, 17 Jul 2019 13:44:55 GMT

←Older revision		Revision as of 13:44, 17 July 2019
Line 1:		Line 1:

	==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==		==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==
-	<StructureSection load='1y9i' size='340' side='right' caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1y9i' size='340' side='right'caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y9/1y9i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y9/1y9i_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 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]		[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]
		+	[[Category: Large Structures]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]
	[[Category: Kumaran, D]]		[[Category: Kumaran, D]]

OCA at 12:14, 12 October 2017

OCA — Thu, 12 Oct 2017 12:14:29 GMT

←Older revision		Revision as of 12:14, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==		==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==
	<StructureSection load='1y9i' size='340' side='right' caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1y9i' size='340' side='right' caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://pdbe.org/1y9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://pdbe.org/1y9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y9i ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 12:20, 8 February 2016

OCA — Mon, 08 Feb 2016 12:20:37 GMT

←Older revision		Revision as of 12:20, 8 February 2016
Line 15:		Line 15:
	<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=1y9i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:30, 10 September 2015

OCA — Thu, 10 Sep 2015 11:30:57 GMT

←Older revision		Revision as of 11:30, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1y9i' size='340' side='right' caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1y9i' size='340' side='right' caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Listeria_monocytogenes Listeria~~ monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://pdbe.org/1y9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1y9i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Listeria~~ monocytogenes]]	+	[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]
	[[Category: Kumaran, D]]		[[Category: Kumaran, D]]

OCA at 13:57, 6 November 2014

OCA — Thu, 06 Nov 2014 13:57:19 GMT

←Older revision		Revision as of 13:57, 6 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: Kumaran, D.]]	+	[[Category: Kumaran, D]]
-	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Swaminathan, S.]]	+	[[Category: Swaminathan, S]]
	[[Category: Helical bundle]]		[[Category: Helical bundle]]
-	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-	~~[[Category: Nysgxrc~~]]	+	[[Category: PSI, Protein structure initiative]]
-	[[Category: Protein structure initiative]]	+
-	~~[[Category: Psi~~]]	+
	[[Category: Putative pgpa]]		[[Category: Putative pgpa]]
-	[[Category: Structural genomic]]
	[[Category: Tetramer]]		[[Category: Tetramer]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 19:19, 29 September 2014

OCA — Mon, 29 Sep 2014 19:19:39 GMT

←Older revision		Revision as of 19:19, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1y9i.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of low temperature requirement C protein from Listeria monocytogenes==
		+	<StructureSection load='1y9i' size='340' side='right' caption='[[1y9i]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y9i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y9I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1y9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y9i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y9i RCSB], [http://www.ebi.ac.uk/pdbsum/1y9i PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1y9i TOPSAN]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y9/1y9i_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 ==
		+	Phosphatidylglycerophosphatase (PGPase), an enzyme involved in lipid metabolism, catalyzes formation of phosphatidylglycerol from phosphatidylglycerophosphate. Phosphatidylglycerol is a multifunctional phospholipid, found in the biological membranes of many organisms. Here, we report the crystal structure of Listeria monocytogenes PGPase at 1.8 A resolution. PGPase, an all-helical molecule, forms a homotetramer. Each protomer contains an independent active site with two metal ions, Ca(2+) and Mg(2+), forming a hetero-binuclear center located in a hydrophilic cavity near the surface of the molecule. The binuclear center, conserved ligands, metal-bound water molecules, and an Asp-His dyad form the active site. The catalytic mechanism of this enzyme is likely to proceed via binuclear metal activated nucleophilic water. The binuclear metal-binding active-site environment of this structure should provide insights into substrate binding and metal-dependent catalysis. A long channel with inter-linked linear water chains, termed "proton wires," is observed at the tetramer interface. Comparison of similar water chain structures in photosynthetic reaction centers (RCs), Cytochrome f, gramicidin, and bacteriorhodopsin, suggests that PGPase may conduct protons via proton wires.

-	~~{{STRUCTURE_1y9i\| PDB=1y9i \| SCENE= }}~~	+	Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires".,Kumaran D, Bonanno JB, Burley SK, Swaminathan S Proteins. 2006 Sep 1;64(4):851-62. PMID:16838328<ref>PMID:16838328</ref>

-	~~===Crystal structure~~ of ~~low temperature requirement C protein from Listeria monocytogenes===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16838328}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1y9i]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Listeria_monocytogenes Listeria monocytogenes]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Y9I OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016838328<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]

OCA at 17:54, 5 January 2013

OCA — Sat, 05 Jan 2013 17:54:16 GMT

←Older revision		Revision as of 17:54, 5 January 2013
Line 1:		Line 1:
	[[Image:1y9i.png\|left\|200px]]		[[Image:1y9i.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1y9i", 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_1y9i\| PDB=1y9i \| SCENE= }}		{{STRUCTURE_1y9i\| PDB=1y9i \| SCENE= }}

	===Crystal structure of low temperature requirement C protein from Listeria monocytogenes===		===Crystal structure of low temperature requirement C protein from Listeria monocytogenes===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16838328}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16838328 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16838328}}		{{ABSTRACT_PUBMED_16838328}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16838328~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016838328</ref><references group="xtra"/>
	[[Category: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]

OCA: Protected "1y9i" [edit=sysop:move=sysop]

OCA — Wed, 29 Dec 2010 18:01:25 GMT

Protected "1y9i" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:01, 29 December 2010