2e6d - Revision history

OCA at 07:56, 13 August 2026

2026-08-13T07:56:47Z

← Older revision		Revision as of 07:56, 13 August 2026
Line 15:		Line 15:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/2e6d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/2e6d_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 08:35, 25 October 2023

2023-10-25T08:35:40Z

← Older revision		Revision as of 08:35, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2e6d' size='340' side='right'caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2e6d' size='340' side='right'caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Trycr Trycr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E6D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E6D FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>~~, ~~<scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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]] 1.94Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">TCDHOD2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Dihydroorotate_oxidase_~~(~~fumarate~~) ~~Dihydroorotate oxidase (fumarate)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1]~~ </~~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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [https://pdbe.org/2e6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [https://www.ebi.ac.uk/pdbsum/2e6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6d 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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [https://pdbe.org/2e6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [https://www.ebi.ac.uk/pdbsum/2e6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PYRD_TRYCC PYRD_TRYCC]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.		[https://www.uniprot.org/uniprot/PYRD_TRYCC PYRD_TRYCC] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Trycr~~]]		[[Category: Trypanosoma cruzi]]
	[[Category: Aoki, T]]		[[Category: Aoki T]]
	[[Category: Harada, S]]		[[Category: Harada S]]
	[[Category: Inaoka~~, D K~~]]		[[Category: Inaoka DK]]
	[[Category: Kita, K]]		[[Category: Kita K]]
	[[Category: Kurisu, G]]		[[Category: Kurisu G]]
	[[Category: Nara, T]]		[[Category: Nara T]]
	[[Category: Sakamoto, K]]		[[Category: Sakamoto K]]
	[[Category: Shiba, T]]		[[Category: Shiba T]]
	[[Category: Shimizu, H]]		[[Category: Shimizu H]]
	~~[[Category: Chagas disease]]~~
	~~[[Category: Dihydroorotate dehydrogenase]]~~
	~~[[Category: Energy metabolism]]~~
	~~[[Category: Flavoprotein]]~~
	~~[[Category: Fumarate reductase]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Pyrimidine biosynthesis]]~~
	~~[[Category: Redox homeostasis~~]]

OCA at 11:49, 10 February 2021

2021-02-10T11:49:39Z

← Older revision		Revision as of 11:49, 10 February 2021
Line 1:		Line 1:

	==Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate==		==Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate==
	<StructureSection load='2e6d' size='340' side='right' caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2e6d' size='340' side='right'caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Trycr Trycr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E6D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trycr Trycr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E6D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [~~http~~://pdbe.org/2e6d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e6d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6d 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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [https://pdbe.org/2e6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [https://www.ebi.ac.uk/pdbsum/2e6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PYRD_TRYCC PYRD_TRYCC]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.		[[https://www.uniprot.org/uniprot/PYRD_TRYCC PYRD_TRYCC]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.
	== 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==
	*[[Dihydroorotate dehydrogenase\|Dihydroorotate dehydrogenase]]		*[[Dihydroorotate dehydrogenase 3D structures\|Dihydroorotate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Trycr]]		[[Category: Trycr]]
	[[Category: Aoki, T]]		[[Category: Aoki, T]]

OCA at 06:36, 6 June 2018

2018-06-06T06:36:50Z

← Older revision		Revision as of 06:36, 6 June 2018
Line 1:		Line 1:

	==Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate==		==Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate==
	<StructureSection load='2e6d' size='340' side='right' caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2e6d' size='340' side='right' caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://pdbe.org/2e6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d 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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://pdbe.org/2e6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/2e6d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/2e6d_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 10:50, 8 February 2016

2016-02-08T10:50:58Z

← Older revision		Revision as of 10:50, 8 February 2016
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=2e6d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:49, 10 September 2015

2015-09-10T10:49:44Z

← Older revision		Revision as of 10:49, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2e6d' size='340' side='right' caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2e6d' size='340' side='right' caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trypanosoma_cruzi Trypanosoma cruzi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trycr Trycr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 ~~Trypanosoma cruzi~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Dihydroorotate_oxidase~~ Dihydroorotate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.1 1.3.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d 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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://pdbe.org/2e6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~Q4D3W2_TRYCR Q4D3W2_TRYCR~~]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.		[[http://www.uniprot.org/uniprot/PYRD_TRYCC PYRD_TRYCC]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 2e6d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Dihydroorotate oxidase]]~~		[[Category: Trycr]]
	~~[[Category: Trypanosoma cruzi~~]]
	[[Category: Aoki, T]]		[[Category: Aoki, T]]
	[[Category: Harada, S]]		[[Category: Harada, S]]

OCA at 22:48, 24 December 2014

2014-12-24T22:48:56Z

← Older revision		Revision as of 22:48, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 Trypanosoma cruzi])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 Trypanosoma cruzi])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase Dihydroorotate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.1 1.3.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase Dihydroorotate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.1 1.3.3.1] </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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d 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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q4D3W2_TRYCR Q4D3W2_TRYCR]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Dihydroorotate oxidase]]		[[Category: Dihydroorotate oxidase]]
	[[Category: Trypanosoma cruzi]]		[[Category: Trypanosoma cruzi]]
	[[Category: Aoki, T.]]		[[Category: Aoki, T]]
	[[Category: Harada, S.]]		[[Category: Harada, S]]
	[[Category: Inaoka, D K.]]		[[Category: Inaoka, D K]]
	[[Category: Kita, K.]]		[[Category: Kita, K]]
	[[Category: Kurisu, G.]]		[[Category: Kurisu, G]]
	[[Category: Nara, T.]]		[[Category: Nara, T]]
	[[Category: Sakamoto, K.]]		[[Category: Sakamoto, K]]
	[[Category: Shiba, T.]]		[[Category: Shiba, T]]
	[[Category: Shimizu, H.]]		[[Category: Shimizu, H]]
	[[Category: Chagas disease]]		[[Category: Chagas disease]]
	[[Category: Dihydroorotate dehydrogenase]]		[[Category: Dihydroorotate dehydrogenase]]

OCA at 08:49, 3 October 2014

2014-10-03T08:49:38Z

← Older revision		Revision as of 08:49, 3 October 2014
Line 1:		Line 1:
	~~{{STRUCTURE_2e6d~~\| ~~PDB~~=2e6d \| ~~SCENE~~= }}		==Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate==
	===~~Crystal~~ structure of Trypanosoma cruzi dihydroorotate ~~dehydrogenase~~ in complex with fumarate~~===~~		<StructureSection load='2e6d' size='340' side='right' caption='[[2e6d]], [[Resolution\|resolution]] 1.94Å' scene=''>
	~~{{ABSTRACT_PUBMED_18808149}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djl\|2djl]], [[2djx\|2djx]], [[2e68\|2e68]], [[2e6a\|2e6a]], [[2e6f\|2e6f]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TCDHOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 Trypanosoma cruzi])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase Dihydroorotate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.1 1.3.3.1] </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=2e6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6d RCSB], [http://www.ebi.ac.uk/pdbsum/2e6d PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/2e6d_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 ==
			Dihydroorotate dehydrogenase (DHOD) from Trypanosoma cruzi (TcDHOD) is a member of family 1A DHOD that catalyzes the oxidation of dihydroorotate to orotate (first half-reaction) and then the reduction of fumarate to succinate (second half-reaction) in the de novo pyrimidine biosynthesis pathway. The oxidation of dihydroorotate is coupled with the reduction of FMN, and the reduced FMN converts fumarate to succinate in the second half-reaction. TcDHOD are known to be essential for survival and growth of T. cruzi and a validated drug target. The first-half reaction mechanism of the family 1A DHOD from Lactococcus lactis has been extensively investigated on the basis of kinetic isotope effects, mutagenesis and X-ray structures determined for ligand-free form and in complex with orotate, the product of the first half-reaction. In this report, we present crystal structures of TcDHOD in the ligand-free form and in complexes with an inhibitor, physiological substrates and products of the first and second half-reactions. These ligands bind to the same active site of TcDHOD, which is consistent with the one-site ping-pong Bi-Bi mechanism demonstrated by kinetic studies for family 1A DHODs. The binding of ligands to TcDHOD does not cause any significant structural changes to TcDHOD, and both reduced and oxidized FMN cofactors are in planar conformation, which indicates that the reduction of the FMN cofactor with dihydroorotate produces anionic reduced FMN. Therefore, they should be good models for the enzymatic reaction pathway of TcDHOD, although orotate and fumarate bind to TcDHOD with the oxidized FMN and dihydroorotate with the reduced FMN in the structures determined here. Cys130, which was identified as the active site base for family 1A DHOD (Fagan, R. L., Jensen, K. F., Bjornberg, O., and Palfey, B. A. (2007) Biochemistry 46, 4028-4036.), is well located for abstracting a proton from dihydroorotate C5 and transferring it to outside water molecules. The bound fumarate is in a twisted conformation, which induces partial charge separation represented as C 2 (delta-) and C 3 (delta+). Because of this partial charge separation, the thermodynamically favorable reduction of fumarate with reduced FMN seems to proceed in the way that C 2 (delta-) accepts a proton from Cys130 and C 3 (delta+) a hydride (or a hydride equivalent) from reduced FMN N 5 in TcDHOD.

	~~==Function==~~		Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction.,Inaoka DK, Sakamoto K, Shimizu H, Shiba T, Kurisu G, Nara T, Aoki T, Kita K, Harada S Biochemistry. 2008 Oct 14;47(41):10881-91. Epub 2008 Sep 23. PMID:18808149<ref>PMID:18808149</ref>
	~~[[http~~:~~//www.uniprot.org/uniprot/Q4D3W2_TRYCR Q4D3W2_TRYCR]] Catalyzes the conversion~~ of dihydroorotate ~~to orotate with~~ fumarate ~~as the electron acceptor~~. ~~Molecular oxygen can replace fumarate in vitro~~.

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[2e6d]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]~~. ~~Full crystallographic information is available from [http:/~~/~~oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA].~~		</div>

	==See Also==		==See Also==
	*[[Dihydroorotate dehydrogenase\|Dihydroorotate dehydrogenase]]		*[[Dihydroorotate dehydrogenase\|Dihydroorotate dehydrogenase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:018808149</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Dihydroorotate oxidase]]		[[Category: Dihydroorotate oxidase]]
	[[Category: Trypanosoma cruzi]]		[[Category: Trypanosoma cruzi]]

OCA at 08:25, 23 April 2014

2014-04-23T08:25:49Z

← Older revision		Revision as of 08:25, 23 April 2014
Line 1:		Line 1:
	~~[[Image:2e6d.png\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2e6d", 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_2e6d\| PDB=2e6d \| SCENE= }}		{{STRUCTURE_2e6d\| PDB=2e6d \| SCENE= }}

	===Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate===		===Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate===
			{{ABSTRACT_PUBMED_18808149}}

			==Function==
	~~<!--~~		[[http://www.uniprot.org/uniprot/Q4D3W2_TRYCR Q4D3W2_TRYCR]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18808149}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 18808149 is~~ the ~~PubMed ID number~~.
	~~-->~~
	~~{{ABSTRACT_PUBMED_18808149}}~~

	==About this Structure==		==About this Structure==
	[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA].		[[2e6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6D OCA].

			==See Also==
			*[[Dihydroorotate dehydrogenase\|Dihydroorotate dehydrogenase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:018808149</ref><references group="xtra"/>		<ref group="xtra">PMID:018808149</ref><references group="xtra"/><references/>
	[[Category: Dihydroorotate oxidase]]		[[Category: Dihydroorotate oxidase]]
	[[Category: Trypanosoma cruzi]]		[[Category: Trypanosoma cruzi]]

OCA: Protected "2e6d" [edit=sysop:move=sysop]

2012-06-02T09:16:59Z

Protected "2e6d" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:16, 2 June 2012
(No difference)