1jry - Revision history

OCA at 08:45, 16 August 2023

2023-08-16T08:45:23Z

←Older revision		Revision as of 08:45, 16 August 2023
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	<StructureSection load='1jry' size='340' side='right'caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1jry' size='340' side='right'caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Acam_591 Acam 591~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JRY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jrx\|1jrx]], [[1jrz\|1jrz]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [https://pdbe.org/1jry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [https://www.ebi.ac.uk/pdbsum/1jry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry 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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [https://pdbe.org/1jry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [https://www.ebi.ac.uk/pdbsum/1jry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FRDA_SHEFR FRDA_SHEFR]] Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.	+	[https://www.uniprot.org/uniprot/FRDA_SHEFR FRDA_SHEFR] Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Acam 591]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Succinate dehydrogenase~~]]	+	[[Category: Shewanella frigidimarina]]
-	[[Category: Chapman~~, S K~~]]	+	[[Category: Chapman SK]]
-	[[Category: Doherty~~, M K~~]]	+	[[Category: Doherty MK]]
-	[[Category: Leys, D]]	+	[[Category: Leys D]]
-	[[Category: Miles~~, C S~~]]	+	[[Category: Miles CS]]
-	[[Category: Mowat~~, C G~~]]	+	[[Category: Mowat CG]]
-	[[Category: Moysey, R]]	+	[[Category: Moysey R]]
-	[[Category: Reid~~, G A~~]]	+	[[Category: Reid GA]]
-	[[Category: Taylor, P]]	+	[[Category: Taylor P]]
-	[[Category: Walkinshaw~~, M D]]~~	+	[[Category: Walkinshaw MD]]
-	~~[[Category: Flavocytochrome]]~~	+
-	~~[[Category: Fumarate reductase]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 14:34, 27 October 2021

2021-10-27T14:34:09Z

OCA at 07:35, 25 November 2020

2020-11-25T07:35:11Z

←Older revision		Revision as of 07:35, 25 November 2020
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	==Crystal structure of Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina==		==Crystal structure of Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina==
-	<StructureSection load='1jry' size='340' side='right' caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1jry' size='340' side='right'caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acam_591 Acam 591]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acam_591 Acam 591]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1JRY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jrx\|1jrx]], [[1jrz\|1jrz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jrx\|1jrx]], [[1jrz\|1jrz]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://pdbe.org/1jry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://pdbe.org/1jry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1jry" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jry" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Flavocytochrome 3D structures\|Flavocytochrome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Acam 591]]		[[Category: Acam 591]]
		+	[[Category: Large Structures]]
	[[Category: Succinate dehydrogenase]]		[[Category: Succinate dehydrogenase]]
	[[Category: Chapman, S K]]		[[Category: Chapman, S K]]

OCA at 08:55, 17 January 2018

2018-01-17T08:55:01Z

←Older revision		Revision as of 08:55, 17 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina==		==Crystal structure of Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina==
	<StructureSection load='1jry' size='340' side='right' caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1jry' size='340' side='right' caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://pdbe.org/1jry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry 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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://pdbe.org/1jry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry 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/jr/1jry_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jr/1jry_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1jry" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jry" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Flavocytochrome\|Flavocytochrome]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:00, 10 February 2016

2016-02-10T03:00:58Z

←Older revision		Revision as of 03:00, 10 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=1jry ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:43, 11 September 2015

2015-09-11T04:43:49Z

←Older revision		Revision as of 04:43, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1jry' size='340' side='right' caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1jry' size='340' side='right' caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Shewanella_frigidimarina Shewanella frigidimarina~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acam_591 Acam 591]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JRY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jrx\|1jrx]], [[1jrz\|1jrz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jrx\|1jrx]], [[1jrz\|1jrz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ~~Shewanella frigidimarina~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry 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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://pdbe.org/1jry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1jry" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Shewanella frigidimarina~~]]	+	[[Category: Acam 591]]
	[[Category: Succinate dehydrogenase]]		[[Category: Succinate dehydrogenase]]
	[[Category: Chapman, S K]]		[[Category: Chapman, S K]]

OCA at 11:20, 25 December 2014

2014-12-25T11:20:22Z

←Older revision		Revision as of 11:20, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JRY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jrx\|1jrx]], [[1jrz\|1jrz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jrx\|1jrx]], [[1jrz\|1jrz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 Shewanella frigidimarina])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 Shewanella frigidimarina])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry 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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FRDA_SHEFR FRDA_SHEFR]] Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Shewanella frigidimarina]]		[[Category: Shewanella frigidimarina]]
	[[Category: Succinate dehydrogenase]]		[[Category: Succinate dehydrogenase]]
-	[[Category: Chapman, S K.]]	+	[[Category: Chapman, S K]]
-	[[Category: Doherty, M K.]]	+	[[Category: Doherty, M K]]
-	[[Category: Leys, D.]]	+	[[Category: Leys, D]]
-	[[Category: Miles, C S.]]	+	[[Category: Miles, C S]]
-	[[Category: Mowat, C G.]]	+	[[Category: Mowat, C G]]
-	[[Category: Moysey, R.]]	+	[[Category: Moysey, R]]
-	[[Category: Reid, G A.]]	+	[[Category: Reid, G A]]
-	[[Category: Taylor, P.]]	+	[[Category: Taylor, P]]
-	[[Category: Walkinshaw, M D.]]	+	[[Category: Walkinshaw, M D]]
	[[Category: Flavocytochrome]]		[[Category: Flavocytochrome]]
	[[Category: Fumarate reductase]]		[[Category: Fumarate reductase]]
	[[Category: Mutant]]		[[Category: Mutant]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 08:36, 28 September 2014

2014-09-28T08:36:51Z

←Older revision		Revision as of 08:36, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1jry.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina==
		+	<StructureSection load='1jry' size='340' side='right' caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JRY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jrx\|1jrx]], [[1jrz\|1jrz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 Shewanella frigidimarina])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [http://www.ebi.ac.uk/pdbsum/1jry 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/jr/1jry_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 ==
		+	There is now overwhelming evidence supporting a common mechanism for fumarate reduction in the respiratory fumarate reductases. The X-ray structures of substrate-bound forms of these enzymes indicate that the substrate is well positioned to accept a hydride from FAD and a proton from an arginine side chain. Recent work on the enzyme from Shewanella frigidimarina [Doherty, M. K., Pealing, S. L., Miles, C. S., Moysey, R., Taylor, P., Walkinshaw, M. D., Reid, G. A., and Chapman, S. K. (2000) Biochemistry 39, 10695-10701] has strengthened the assignment of an arginine (Arg402) as the proton donor in fumarate reduction. Here we describe the crystallographic and kinetic analyses of the R402A, R402K, and R402Y mutant forms of the Shewanella enzyme. The crystal structure of the R402A mutant (2.0 A resolution) shows it to be virtually identical to the wild-type enzyme, apart from the fact that a water molecule occupies the position previously taken by part of the guanidine group of R402. Although structurally similar to the wild-type enzyme, the R402A mutant is inactive under all the conditions that were studied. This implies that a water molecule, in this position in the active site, cannot function as the proton donor for fumarate reduction. In contrast to the R402A mutation, both the R402K and R402Y mutant enzymes are active. Although this activity was at a very low level (at pH 7.2 some 10(4)-fold lower than that for the wild type), it does imply that both lysine and tyrosine can fulfill the role of an active site proton donor, albeit very poorly. The crystal structures of the R402K and R402Y mutant enzymes (2.0 A resolution) show that distances from the lysine and tyrosine side chains to the nearest carbon atom of fumarate are approximately 3.5 A, clearly permitting proton transfer. The combined results from mutagenesis, crystallographic, and kinetic studies provide formidable evidence that R402 acts as both a Lewis acid (stabilizing the build-up of negative charge upon hydride transfer from FAD to fumarate) and a Bronsted acid (donating the proton to the substrate to complete the formation of succinate).

-	~~{{STRUCTURE_1jry\| PDB=1jry \| SCENE= }}~~	+	Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase.,Mowat CG, Moysey R, Miles CS, Leys D, Doherty MK, Taylor P, Walkinshaw MD, Reid GA, Chapman SK Biochemistry. 2001 Oct 16;40(41):12292-8. PMID:11591148<ref>PMID:11591148</ref>

-	~~===Crystal structure~~ of ~~Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11591148}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1jry]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA].~~	+

	==See Also==		==See Also==
	*[[Flavocytochrome\|Flavocytochrome]]		*[[Flavocytochrome\|Flavocytochrome]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011591148<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Shewanella frigidimarina]]		[[Category: Shewanella frigidimarina]]
	[[Category: Succinate dehydrogenase]]		[[Category: Succinate dehydrogenase]]

OCA at 16:05, 20 October 2012

2012-10-20T16:05:42Z

←Older revision		Revision as of 16:05, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1jry]] is a 2 chain structure ~~of [[Flavocytochrome]]~~ with sequence from [http://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA].	+	[[1jry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA].

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

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

2012-07-26T20:35:22Z

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

←Older revision

Revision as of 20:35, 26 July 2012

←Older revision		Revision as of 14:34, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1jry' size='340' side='right'caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1jry' size='340' side='right'caption='[[1jry]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Acam_591 Acam 591]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1JRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jry]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acam_591 Acam 591]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JRY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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;'>[[1jrx\|1jrx]], [[1jrz\|1jrz]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jrx\|1jrx]], [[1jrz\|1jrz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcc ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56812 ACAM 591])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [~~http~~://pdbe.org/1jry PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jry PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry 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=1jry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jry OCA], [https://pdbe.org/1jry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jry RCSB], [https://www.ebi.ac.uk/pdbsum/1jry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jry ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FRDA_SHEFR FRDA_SHEFR]] Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.	+	[[https://www.uniprot.org/uniprot/FRDA_SHEFR FRDA_SHEFR]] Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]