2yvg - Revision history

OCA at 13:54, 13 March 2024

2024-03-13T13:54:58Z

←Older revision		Revision as of 13:54, 13 March 2024
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	<StructureSection load='2yvg' size='340' side='right'caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2yvg' size='340' side='right'caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Achromobacter_georgiopolitanum Achromobacter georgiopolitanum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YVG 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2yvf\|2yvf]]</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>bphA4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~306 Achromobacter georgiopolitanum])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Ferredoxin~~--~~NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2]~~ </~~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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [https://pdbe.org/2yvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [https://www.ebi.ac.uk/pdbsum/2yvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvg 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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [https://pdbe.org/2yvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [https://www.ebi.ac.uk/pdbsum/2yvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q52437_PSES1 Q52437_PSES1]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2yvg 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=2yvg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation. In order to elucidate the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. In addition, the conformational changes induced by the preceding electron transfer seem to induce the next electron transfer. The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron-transfer reaction from NADH to BphA3.
-
-	Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin.,Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T J Mol Biol. 2007 Oct 19;373(2):382-400. Epub 2007 Aug 19. PMID:17850818<ref>PMID:17850818</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2yvg" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Achromobacter georgiopolitanum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Senda, M~~]]	+	[[Category: Pseudomonas sp]]
-	[[Category: Senda~~, T~~]]	+	[[Category: Senda M]]
-	[[Category: ~~Flavoprotein]]~~	+	[[Category: Senda T]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:40, 8 December 2021

2021-12-08T10:40:45Z

←Older revision		Revision as of 10:40, 8 December 2021
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	==crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)==		==crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)==
-	<StructureSection load='2yvg' size='340' side='right' caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2yvg' size='340' side='right'caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Achromobacter_georgiopolitanum Achromobacter georgiopolitanum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_georgiopolitanum Achromobacter georgiopolitanum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YVG 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yvf\|2yvf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2yvf\|2yvf]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Achromobacter georgiopolitanum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Achromobacter georgiopolitanum])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [~~http~~://pdbe.org/2yvg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yvg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvg 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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [https://pdbe.org/2yvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [https://www.ebi.ac.uk/pdbsum/2yvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter georgiopolitanum]]		[[Category: Achromobacter georgiopolitanum]]
		+	[[Category: Large Structures]]
	[[Category: Senda, M]]		[[Category: Senda, M]]
	[[Category: Senda, T]]		[[Category: Senda, T]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 09:34, 17 October 2018

2018-10-17T09:34:45Z

←Older revision		Revision as of 09:34, 17 October 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/2yvg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/2yvg_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 11:25, 11 August 2016

2016-08-11T11:25:16Z

←Older revision		Revision as of 11:25, 11 August 2016
Line 1:		Line 1:
		+
	==crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)==		==crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)==
	<StructureSection load='2yvg' size='340' side='right' caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2yvg' size='340' side='right' caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_sp. Pseudomonas sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_georgiopolitanum Achromobacter georgiopolitanum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YVG 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yvf\|2yvf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yvf\|2yvf]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 ~~Pseudomonas sp.~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Achromobacter georgiopolitanum])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [http://www.ebi.ac.uk/pdbsum/2yvg 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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [http://pdbe.org/2yvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [http://www.ebi.ac.uk/pdbsum/2yvg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 18:
	<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=2yvg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		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 2yvg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas sp~~]]	+	[[Category: Achromobacter georgiopolitanum]]
	[[Category: Senda, M]]		[[Category: Senda, M]]
	[[Category: Senda, T]]		[[Category: Senda, T]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 08:43, 20 January 2015

2015-01-20T08:43:39Z

←Older revision		Revision as of 08:43, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YVG 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yvf\|2yvf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yvf\|2yvf]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Pseudomonas sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Pseudomonas sp.])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [http://www.ebi.ac.uk/pdbsum/2yvg 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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [http://www.ebi.ac.uk/pdbsum/2yvg 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 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pseudomonas sp.]]	+	[[Category: Pseudomonas sp]]
-	[[Category: Senda, M.]]	+	[[Category: Senda, M]]
-	[[Category: Senda, T.]]	+	[[Category: Senda, T]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 05:13, 2 October 2014

2014-10-02T05:13:41Z

←Older revision		Revision as of 05:13, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2yvg.~~png~~\|~~left~~\|200px]]	+	==crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)==
		+	<StructureSection load='2yvg' size='340' side='right' caption='[[2yvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YVG 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yvf\|2yvf]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Pseudomonas sp.])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </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=2yvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yvg RCSB], [http://www.ebi.ac.uk/pdbsum/2yvg 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/yv/2yvg_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 ==
		+	The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation. In order to elucidate the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. In addition, the conformational changes induced by the preceding electron transfer seem to induce the next electron transfer. The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron-transfer reaction from NADH to BphA3.

-	~~{{STRUCTURE_2yvg\| PDB=2yvg \| SCENE= }}~~	+	Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin.,Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T J Mol Biol. 2007 Oct 19;373(2):382-400. Epub 2007 Aug 19. PMID:17850818<ref>PMID:17850818</ref>

-	~~===crystal structure of ferredoxin reductase~~, ~~BPHA4 (blue-semiquinone)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17850818}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2yvg]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_sp~~. ~~Pseudomonas sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017850818<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pseudomonas sp.]]		[[Category: Pseudomonas sp.]]
	[[Category: Senda, M.]]		[[Category: Senda, M.]]

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

2013-01-07T21:09:56Z

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

←Older revision

Revision as of 21:09, 7 January 2013

OCA at 21:09, 7 January 2013

2013-01-07T21:09:52Z

←Older revision		Revision as of 21:09, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2yvg.png\|left\|200px]]		[[Image:2yvg.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2yvg", 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_2yvg\| PDB=2yvg \| SCENE= }}		{{STRUCTURE_2yvg\| PDB=2yvg \| SCENE= }}

	===crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)===		===crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17850818}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17850818 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17850818}}		{{ABSTRACT_PUBMED_17850818}}

	==About this Structure==		==About this Structure==
-	~~2YVG~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA].	+	[[2yvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17850818~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017850818</ref><references group="xtra"/>
	[[Category: Pseudomonas sp.]]		[[Category: Pseudomonas sp.]]
	[[Category: Senda, M.]]		[[Category: Senda, M.]]
Line 29:		Line 17:
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:17:49 2009''

OCA at 22:17, 17 February 2009

2009-02-17T22:17:50Z

←Older revision		Revision as of 22:17, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2YVG is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA].	+	2YVG is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVG OCA].

	==Reference==		==Reference==
-	Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin., Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T, J Mol Biol. 2007 Oct 19;373(2):382-400. Epub 2007 Aug 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17850818 17850818]~~	+	<ref group="xtra">PMID:17850818</ref><references group="xtra"/>
	[[Category: Pseudomonas sp.]]		[[Category: Pseudomonas sp.]]
-	[[Category: Single protein]]
	[[Category: Senda, M.]]		[[Category: Senda, M.]]
	[[Category: Senda, T.]]		[[Category: Senda, T.]]
Line 31:		Line 30:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:38:~~41 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:17:49 2009''

OCA at 04:38, 29 July 2008

2008-07-29T04:38:44Z

←Older revision		Revision as of 04:38, 29 July 2008
Line 1:		Line 1:
-	[[Image:2yvg.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2yvg.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2yvg\| PDB=2yvg \| SCENE= }}		{{STRUCTURE_2yvg\| PDB=2yvg \| SCENE= }}

-	~~'''~~crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)~~'''~~	+	===crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone)===


-	~~==Overview==~~	+	<!--
-	~~The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD~~-~~containing NADH~~-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The ~~reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2~~, ~~a terminal oxygenase~~, ~~to support~~ the ~~activation of dioxygen for biphenyl dihydroxylation. In order~~ to ~~elucidate~~ the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. ~~In addition~~, the ~~conformational changes induced by the preceding electron transfer seem to induce the next electron transfer~~. ~~The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron~~-~~transfer reaction from NADH to BphA3.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17850818}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17850818 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17850818}}

	==About this Structure==		==About this Structure==
Line 26:		Line 30:
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 19~~:31:57 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 07:38:41 2008''