2e25 - Revision history

OCA at 08:33, 25 October 2023

2023-10-25T08:33:47Z

←Older revision		Revision as of 08:33, 25 October 2023
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	<StructureSection load='2e25' size='340' side='right'caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2e25' size='340' side='right'caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e25]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e25]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E25 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FOT:5~~-~~FLUORO-2,6-DIOXO-1~~,2~~,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~KCX~~:~~LYSINE+NZ~~-CARBOXYLIC+ACID'>~~KCX~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1xge\|1xge]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">PYRC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [https://pdbe.org/2e25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [https://www.ebi.ac.uk/pdbsum/2e25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e25 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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [https://pdbe.org/2e25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [https://www.ebi.ac.uk/pdbsum/2e25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e25 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PYRC_ECOLI PYRC_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2e25" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2e25" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydroorotase 3D structures\|Dihydroorotase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Dihydroorotase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Guss~~, J M~~]]	+	[[Category: Guss JM]]
-	[[Category: Lee, M]]	+	[[Category: Lee M]]
-	[[Category: Maher~~, M J]]~~	+	[[Category: Maher MJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 11:44, 10 February 2021

2021-02-10T11:44:46Z

←Older revision		Revision as of 11:44, 10 February 2021
Line 1:		Line 1:

	==The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate==		==The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate==
-	<StructureSection load='2e25' size='340' side='right' caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2e25' size='340' side='right'caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e25]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E25 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e25]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E25 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xge\|1xge]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xge\|1xge]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [~~http~~://pdbe.org/2e25 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e25 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e25 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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [https://pdbe.org/2e25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [https://www.ebi.ac.uk/pdbsum/2e25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e25 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 36:		Line 36:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Dihydroorotase]]		[[Category: Dihydroorotase]]
		+	[[Category: Large Structures]]
	[[Category: Guss, J M]]		[[Category: Guss, J M]]
	[[Category: Lee, M]]		[[Category: Lee, M]]

OCA at 06:34, 6 June 2018

2018-06-06T06:34:32Z

←Older revision		Revision as of 06:34, 6 June 2018
Line 1:		Line 1:
		+
	==The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate==		==The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate==
	<StructureSection load='2e25' size='340' side='right' caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2e25' size='340' side='right' caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://pdbe.org/2e25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://pdbe.org/2e25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e25 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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/e2/2e25_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e25_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=2e25 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:21, 11 September 2015

2015-09-11T17:21:15Z

←Older revision		Revision as of 17:21, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2e25' size='340' side='right' caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2e25' size='340' side='right' caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e25]] is a 1 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=2E25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E25 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xge\|1xge]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xge\|1xge]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([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">PYRC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://pdbe.org/2e25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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 2e25" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Dihydroorotase]]		[[Category: Dihydroorotase]]
-	[[Category: Escherichia coli]]
	[[Category: Guss, J M]]		[[Category: Guss, J M]]
	[[Category: Lee, M]]		[[Category: Lee, M]]

OCA at 17:31, 15 January 2015

2015-01-15T17:31:19Z

←Older revision		Revision as of 17:31, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e25]] is a 1 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=2E25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E25 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e25]] is a 1 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=2E25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E25 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xge\|1xge]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xge\|1xge]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([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">PYRC ([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/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Dihydroorotase]]		[[Category: Dihydroorotase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Guss, J M.]]	+	[[Category: Guss, J M]]
-	[[Category: Lee, M.]]	+	[[Category: Lee, M]]
-	[[Category: Maher, M J.]]	+	[[Category: Maher, M J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 00:44, 30 September 2014

2014-09-30T00:44:43Z

←Older revision		Revision as of 00:44, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2e25.~~png~~\|~~left~~\|200px]]	+	==The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate==
		+	<StructureSection load='2e25' size='340' side='right' caption='[[2e25]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2e25]] is a 1 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=2E25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E25 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOT:5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>FOT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xge\|1xge]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYRC ([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/Dihydroorotase Dihydroorotase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.3 3.5.2.3] </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=2e25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e25 RCSB], [http://www.ebi.ac.uk/pdbsum/2e25 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/e2/2e25_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 ==
		+	Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of L-dihydroorotate (L-DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001), Biochemistry, 40, 6989-6997; Lee et al. (2005), J. Mol. Biol. 348, 523-533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N-carbamyl-L-aspartate (L-CA-asp) and the active site of the other monomer contains the product of the reaction, L-DHO. In the subunit with L-DHO in the active site, a surface loop (residues 105-115) is 'open'. In the other subunit, with L-CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the L-CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (L-DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P4(1)2(1)2, with unit-cell parameters a = b = 72.6, c = 176.1 A. The structure has been refined to R and R(free) values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the 'open' conformation, which is consistent with FOA, like L-DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of L-DHO is explained by initial binding of L-DHO to both subunits, followed by slow conversion to L-CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of L-DHO and L-CA-asp.

-	~~{{STRUCTURE_2e25\| PDB=2e25 \| SCENE= }}~~	+	Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal form.,Lee M, Maher MJ, Guss JM Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Mar 1;63(Pt, 3):154-61. Epub 2007 Feb 13. PMID:17329804<ref>PMID:17329804</ref>

-	~~===The Crystal Structure~~ of the ~~T109S mutant~~ of E. ~~coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17329804}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2e25]] is a 1 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=2E25 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017329804<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Dihydroorotase]]		[[Category: Dihydroorotase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "2e25" [edit=sysop:move=sysop]

2013-01-06T10:05:33Z

Protected "2e25" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:05, 6 January 2013

OCA at 10:05, 6 January 2013

2013-01-06T10:05:29Z

←Older revision		Revision as of 10:05, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2e25.png\|left\|200px]]		[[Image:2e25.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2e25", 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_2e25\| PDB=2e25 \| SCENE= }}		{{STRUCTURE_2e25\| PDB=2e25 \| SCENE= }}

	===The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate===		===The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17329804}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17329804 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17329804}}		{{ABSTRACT_PUBMED_17329804}}

	==About this Structure==		==About this Structure==
-	~~2E25~~ is a 1 chain structure of 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=2E25 OCA].	+	[[2e25]] is a 1 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=2E25 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17329804~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017329804</ref><references group="xtra"/>
	[[Category: Dihydroorotase]]		[[Category: Dihydroorotase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 29:		Line 17:
	[[Category: Lee, M.]]		[[Category: Lee, M.]]
	[[Category: Maher, M J.]]		[[Category: Maher, M J.]]
		+	[[Category: Hydrolase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:39:53 2009''

OCA at 02:39, 18 February 2009

2009-02-18T02:39:54Z

←Older revision		Revision as of 02:39, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2E25 is a ~~[[Single protein]]~~ structure of 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=2E25 OCA].	+	2E25 is a 1 chain structure of 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=2E25 OCA].

	==Reference==		==Reference==
-	Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal form., Lee M, Maher MJ, Guss JM, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Mar 1;63(Pt, 3):154-61. Epub 2007 Feb 13. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17329804 17329804]~~	+	<ref group="xtra">PMID:17329804</ref><references group="xtra"/>
	[[Category: Dihydroorotase]]		[[Category: Dihydroorotase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Guss, J M.]]		[[Category: Guss, J M.]]
	[[Category: Lee, M.]]		[[Category: Lee, M.]]
Line 32:		Line 31:
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 11~~:25:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:39:53 2009''

OCA at 08:25, 29 July 2008

2008-07-29T08:25:27Z

←Older revision		Revision as of 08:25, 29 July 2008
Line 1:		Line 1:
-	[[Image:2e25.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2e25.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2e25\| PDB=2e25 \| SCENE= }}		{{STRUCTURE_2e25\| PDB=2e25 \| SCENE= }}

-	~~'''~~The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate~~'''~~	+	===The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate===


-	~~==Overview==~~	+	<!--
-	~~Crystals of a single~~-~~point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of L~~-~~dihydroorotate (L-DHO) are tetragonal~~, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001), Biochemistry, 40, 6989-6997; Lee et al. (2005), J. Mol. Biol. 348, 523-533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N-carbamyl-L-aspartate (L-CA-asp) and the active site of the other monomer contains the product of the reaction, L-DHO. In the subunit with L-DHO in the active site, a surface loop (residues 105-115) is 'open'. In the other subunit, with L-CA-asp in the active site, the loop folds inwards, ~~forming specific hydrogen bonds from~~ the ~~loop~~ to the ~~L-CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate~~ (~~FOA), a product (L-DHO) mimic~~. ~~Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P4(1)2(1)2, with unit-cell parameters a = b = 72~~.~~6, c = 176.1 A. The structure has been refined to R and R(free~~) ~~values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the 'open' conformation~~, ~~which~~ is ~~consistent with FOA, like L-DHO, binding at both sites. The behaviour of~~ the T109S mutant crystals of DHOase in the presence of L-DHO is explained by initial binding of L-DHO to both subunits, followed by slow conversion to L-CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. ~~Orthorhombic crystals are then able to grow in the presence of L~~-~~DHO and L~~-~~CA-asp.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17329804}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17329804 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17329804}}

	==About this Structure==		==About this Structure==
Line 27:		Line 31:
	[[Category: Maher, M J.]]		[[Category: Maher, M J.]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 01~~:46:58 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:25:20 2008''