3lq4 - Revision history

OCA at 08:42, 6 September 2023

OCA — Wed, 06 Sep 2023 08:42:14 GMT

←Older revision		Revision as of 08:42, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3lq4' size='340' side='right'caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='3lq4' size='340' side='right'caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Eco57 Eco57~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 1.98Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [https://pdbe.org/3lq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [https://www.ebi.ac.uk/pdbsum/3lq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lq4 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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [https://pdbe.org/3lq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [https://www.ebi.ac.uk/pdbsum/3lq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lq4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ODP1_ECO57 ODP1_ECO57]] Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity).	+	[https://www.uniprot.org/uniprot/ODP1_ECO57 ODP1_ECO57] Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eco57~~]]	+	[[Category: Escherichia coli O157:H7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Furey, W]]	+	[[Category: Furey W]]
-	~~[[Category: Glycolysis]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pyruvate]]~~	+
-	~~[[Category: Pyruvate dehydrogenase]]~~	+
-	~~[[Category: Thdp]]~~	+
-	~~[[Category: Thiamine pyrophosphate~~]]	+

OCA at 10:24, 4 August 2021

OCA — Wed, 04 Aug 2021 10:24:25 GMT

←Older revision		Revision as of 10:24, 4 August 2021
Line 1:		Line 1:

	==E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration==		==E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration==
-	<StructureSection load='3lq4' size='340' side='right' caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='3lq4' size='340' side='right'caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=~~TDP~~:~~THIAMIN~~+DIPHOSPHATE'>~~TDP~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_(acetyl-transferring) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [~~http~~://pdbe.org/3lq4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lq4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lq4 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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [https://pdbe.org/3lq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [https://www.ebi.ac.uk/pdbsum/3lq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lq4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ODP1_ECO57 ODP1_ECO57]] Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity).	+	[[https://www.uniprot.org/uniprot/ODP1_ECO57 ODP1_ECO57]] Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Pyruvate dehydrogenase\|Pyruvate dehydrogenase]]	+	*[[Pyruvate dehydrogenase 3D structures\|Pyruvate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Eco57]]		[[Category: Eco57]]
		+	[[Category: Large Structures]]
	[[Category: Furey, W]]		[[Category: Furey, W]]
	[[Category: Glycolysis]]		[[Category: Glycolysis]]

OCA at 07:49, 9 January 2019

OCA — Wed, 09 Jan 2019 07:49:27 GMT

←Older revision		Revision as of 07:49, 9 January 2019
Line 1:		Line 1:
		+
	==E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration==		==E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration==
	<StructureSection load='3lq4' size='340' side='right' caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='3lq4' size='340' side='right' caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_(acetyl-transferring) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://pdbe.org/3lq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://pdbe.org/3lq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lq4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lq/3lq4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lq/3lq4_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:46, 7 February 2016

OCA — Sun, 07 Feb 2016 03:46:59 GMT

←Older revision		Revision as of 03:46, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3lq4' size='340' side='right' caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='3lq4' size='340' side='right' caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_(acetyl-transferring) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://pdbe.org/3lq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=3lq4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3lq4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Eco57]]
	[[Category: Furey, W]]		[[Category: Furey, W]]
	[[Category: Glycolysis]]		[[Category: Glycolysis]]

OCA at 07:37, 24 December 2014

OCA — Wed, 24 Dec 2014 07:37:34 GMT

←Older revision		Revision as of 07:37, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_(acetyl-transferring) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ODP1_ECO57 ODP1_ECO57]] Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Furey, W.]]	+	[[Category: Furey, W]]
	[[Category: Glycolysis]]		[[Category: Glycolysis]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]

OCA at 11:23, 29 September 2014

OCA — Mon, 29 Sep 2014 11:23:47 GMT

←Older revision		Revision as of 11:23, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3lq4.~~png~~\|~~left~~\|200px]]	+	==E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration==
		+	<StructureSection load='3lq4' size='340' side='right' caption='[[3lq4]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LQ4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iea\|2iea]], [[3lpl\|3lpl]], [[3lq2\|3lq2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aceE, B0114, ECs0118, Z0124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3lq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lq4 RCSB], [http://www.ebi.ac.uk/pdbsum/3lq4 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/lq/3lq4_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 ==
		+	Kinetic, spectroscopic, and structural analysis tested the hypothesis that a chain of residues connecting the 4'-aminopyrimidine N1' atoms of thiamin diphosphates (ThDPs) in the two active centers of the Escherichia coli pyruvate dehydrogenase complex E1 component provides a signal transduction pathway. Substitution of the three acidic residues (Glu(571), Glu(235), and Glu(237)) and Arg(606) resulted in impaired binding of the second ThDP, once the first active center was filled, suggesting a pathway for communication between the two ThDPs. 1) Steady-state kinetic and fluorescence quenching studies revealed that upon E571A, E235A, E237A, and R606A substitutions, ThDP binding in the second active center was affected. 2) Analysis of the kinetics of thiazolium C2 hydrogen/deuterium exchange of enzyme-bound ThDP suggests half-of-the-sites reactivity for the E1 component, with fast (activated site) and slow exchanging sites (dormant site). The E235A and E571A variants gave no evidence for the slow exchanging site, indicating that only one of two active sites is filled with ThDP. 3) Titration of the E235A and E237A variants with methyl acetylphosphonate monitored by circular dichroism suggested that only half of the active sites were filled with a covalent predecarboxylation intermediate analog. 4) Crystal structures of E235A and E571A in complex with ThDP revealed the structural basis for the spectroscopic and kinetic observations and showed that either substitution affects cofactor binding, despite the fact that Glu(235) makes no direct contact with the cofactor. The role of the conserved Glu(571) residue in both catalysis and cofactor orientation is revealed by the combined results for the first time.

-	~~{{STRUCTURE_3lq4\| PDB=3lq4 \| SCENE= }}~~	+	Communication between thiamin cofactors in the Escherichia coli pyruvate dehydrogenase complex E1 component active centers: evidence for a "direct pathway" between the 4'-aminopyrimidine N1' atoms.,Nemeria NS, Arjunan P, Chandrasekhar K, Mossad M, Tittmann K, Furey W, Jordan F J Biol Chem. 2010 Apr 9;285(15):11197-209. Epub 2010 Jan 27. PMID:20106967<ref>PMID:20106967</ref>

-	~~===E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20106967}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3lq4]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].~~	+

	==See Also==		==See Also==
	*[[Pyruvate dehydrogenase\|Pyruvate dehydrogenase]]		*[[Pyruvate dehydrogenase\|Pyruvate dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020106967<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Furey, W.]]		[[Category: Furey, W.]]

OCA at 05:30, 20 October 2012

OCA — Sat, 20 Oct 2012 05:30:23 GMT

←Older revision		Revision as of 05:30, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3lq4]] is a 2 chain structure ~~of [[Pyruvate dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].	+	[[3lq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].

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

OCA: Protected "3lq4" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 10:16:23 GMT

Protected "3lq4" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:16, 25 July 2012

OCA at 10:16, 25 July 2012

OCA — Wed, 25 Jul 2012 10:16:22 GMT

←Older revision		Revision as of 10:16, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3lq4.png\|left\|200px]]		[[Image:3lq4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lq4", 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_3lq4\| PDB=3lq4 \| SCENE= }}		{{STRUCTURE_3lq4\| PDB=3lq4 \| SCENE= }}

	===E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration===		===E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20106967}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20106967 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20106967}}		{{ABSTRACT_PUBMED_20106967}}

	==About this Structure==		==About this Structure==
-	~~3LQ4~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].	+	[[3lq4]] is a 2 chain structure of [[Pyruvate dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].
		+
		+	==See Also==
		+	*[[Pyruvate dehydrogenase\|Pyruvate dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20106967~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020106967</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Furey, W.]]		[[Category: Furey, W.]]
Line 33:		Line 24:
	[[Category: Thdp]]		[[Category: Thdp]]
	[[Category: Thiamine pyrophosphate]]		[[Category: Thiamine pyrophosphate]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 09:12:43 2010''

OCA at 06:12, 21 April 2010

OCA — Wed, 21 Apr 2010 06:12:44 GMT

←Older revision		Revision as of 06:12, 21 April 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3lq4.~~jpg~~\|left\|200px]]	+	[[Image:3lq4.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration===		===E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20106967}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20106967 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20106967}}

	==About this Structure==		==About this Structure==
	3LQ4 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].		3LQ4 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LQ4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20106967</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Furey, W.]]		[[Category: Furey, W.]]
Line 25:		Line 34:
	[[Category: Thiamine pyrophosphate]]		[[Category: Thiamine pyrophosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 3 17~~:27:34 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 09:12:43 2010''