1akq - Revision history

OCA at 06:31, 7 February 2024

OCA — Wed, 07 Feb 2024 06:31:25 GMT

←Older revision		Revision as of 06:31, 7 February 2024
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	<StructureSection load='1akq' size='340' side='right'caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1akq' size='340' side='right'caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Desvh Desvh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AKQ 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></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]] 1.9Å</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></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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [https://pdbe.org/1akq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [https://www.ebi.ac.uk/pdbsum/1akq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1akq 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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [https://pdbe.org/1akq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [https://www.ebi.ac.uk/pdbsum/1akq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1akq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH]] Low-potential electron donor to a number of redox enzymes.	+	[https://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH] Low-potential electron donor to a number of redox enzymes.
	== 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=1akq 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=1akq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The side chain of aspartate 95 in flavodoxin from Desulfovibrio vulgaris provides the closest negative charge to N(1) of the bound FMN in the protein. Site-directed mutagenesis was used to substitute alanine, asparagine, or glutamate for this amino acid to assess the effect of this charge on the semiquinone/hydroquinone redox potential (E(1)) of the FMN cofactor. The D95A mutation shifts the E(1) redox potential positively by 16 mV, while a negative shift of 23 mV occurs in the oxidized/semiquinone midpoint redox potential (E(2)). The crystal structures of the oxidized and semiquinone forms of this mutant are similar to the corresponding states of the wild-type protein. In contrast to the wild-type protein, a further change in structure occurs in the D95A mutant in the hydroquinone form. The side chain of Y98 flips into an energetically more favorable edge-to-face interaction with the bound FMN. Analysis of the structural changes in the D95A mutant, taking into account electrostatic interactions at the FMN binding site, suggests that the pi-pi electrostatic repulsions have only a minor contribution to the very low E(1) redox potential of the FMN cofactor when bound to apoflavodoxin. Substitution of D95 with glutamate causes only a slight perturbation of the two one-electron redox potentials of the FMN cofactor. The structure of the D95E mutant reveals a large movement of the 60-loop (residues 60-64) away from the flavin in the oxidized structure. Reduction of this mutant to the hydroquinone causes the conformation of the 60-loop to revert back to that occurring in the structures of the wild-type protein. The crystal structures of the D95E mutant imply that electrostatic repulsion between a carboxylate on the side chain at position 95 and the phenol ring of Y98 prevents rotation of the Y98 side chain to a more energetically favorable conformation as occurs in the D95A mutant. Replacement of D95 with asparagine has no effect on E(2) but causes E(1) to change by 45 mV. The D95N mutant failed to crystallize. The K(d) values of the protein FMN complex in all three oxidation-reduction states differ from those of the wild-type complexes. Molecular modeling showed that the conformational energy of the protein changes with the redox state, in qualitative agreement with the observed changes in K(d), and allowed the electrostatic interactions between the FMN and the surrounding groups on the protein to be quantified.
-
-	Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin.,McCarthy AA, Walsh MA, Verma CS, O'Connell DP, Reinhold M, Yalloway GN, D'Arcy D, Higgins TM, Voordouw G, Mayhew SG Biochemistry. 2002 Sep 10;41(36):10950-62. PMID:12206666<ref>PMID:12206666</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1akq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Flavodoxin 3D structures\|Flavodoxin 3D structures]]		*[[Flavodoxin 3D structures\|Flavodoxin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desvh~~]]	+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Higgins, T]]	+	[[Category: Higgins T]]
-	[[Category: Mccarthy, A]]	+	[[Category: Mccarthy A]]
-	[[Category: Walsh, M]]	+	[[Category: Walsh M]]
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Flavodoxin]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Fmn]]~~	+
-	~~[[Category: Mutant~~]]	+

OCA at 09:46, 26 May 2021

OCA — Wed, 26 May 2021 09:46:30 GMT

←Older revision		Revision as of 09:46, 26 May 2021
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	<StructureSection load='1akq' size='340' side='right'caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1akq' size='340' side='right'caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AKQ 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></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></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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [~~http~~://pdbe.org/1akq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1akq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1akq 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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [https://pdbe.org/1akq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [https://www.ebi.ac.uk/pdbsum/1akq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1akq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH]] Low-potential electron donor to a number of redox enzymes.	+	[[https://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH]] Low-potential electron donor to a number of redox enzymes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:19, 21 August 2019

OCA — Wed, 21 Aug 2019 07:19:01 GMT

←Older revision		Revision as of 07:19, 21 August 2019
Line 1:		Line 1:

	==D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS==		==D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS==
-	<StructureSection load='1akq' size='340' side='right' caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1akq' size='340' side='right'caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/1akq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/1akq_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 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1akq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1akq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Flavodoxin 3D structures\|Flavodoxin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Desvh]]		[[Category: Desvh]]
		+	[[Category: Large Structures]]
	[[Category: Higgins, T]]		[[Category: Higgins, T]]
	[[Category: Mccarthy, A]]		[[Category: Mccarthy, A]]

OCA at 10:44, 15 November 2017

OCA — Wed, 15 Nov 2017 10:44:43 GMT

←Older revision		Revision as of 10:44, 15 November 2017
Line 1:		Line 1:
		+
	==D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS==		==D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS==
	<StructureSection load='1akq' size='340' side='right' caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1akq' size='340' side='right' caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ 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></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></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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://pdbe.org/1akq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq 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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://pdbe.org/1akq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1akq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1akq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1akq" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Flavodoxin\|Flavodoxin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:04, 9 February 2016

OCA — Tue, 09 Feb 2016 11:04:06 GMT

←Older revision		Revision as of 11:04, 9 February 2016
Line 16:		Line 16:
	<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=1akq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:40, 10 September 2015

OCA — Thu, 10 Sep 2015 21:40:52 GMT

←Older revision		Revision as of 21:40, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1akq' size='340' side='right' caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1akq' size='340' side='right' caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ 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></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></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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq 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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://pdbe.org/1akq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1akq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris str. hildenborough~~]]	+	[[Category: Desvh]]
	[[Category: Higgins, T]]		[[Category: Higgins, T]]
	[[Category: Mccarthy, A]]		[[Category: Mccarthy, A]]

OCA at 06:27, 25 December 2014

OCA — Thu, 25 Dec 2014 06:27:58 GMT

←Older revision		Revision as of 06:27, 25 December 2014
Line 6:		Line 6:
	<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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq 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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH]] Low-potential electron donor to a number of redox enzymes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:38, 22 December 2014

OCA — Mon, 22 Dec 2014 11:38:54 GMT

←Older revision		Revision as of 11:38, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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></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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq 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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq 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 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
-	[[Category: Higgins, T.]]	+	[[Category: Higgins, T]]
-	[[Category: Mccarthy, A.]]	+	[[Category: Mccarthy, A]]
-	[[Category: Walsh, M.]]	+	[[Category: Walsh, M]]
	[[Category: Electron transfer]]		[[Category: Electron transfer]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 08:13, 30 July 2014

OCA — Wed, 30 Jul 2014 08:13:26 GMT

←Older revision		Revision as of 08:13, 30 July 2014
Line 1:		Line 1:
-	[[~~Image~~:1akq.~~png\|left~~\|200px]]	+	==D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS==
		+	<StructureSection load='1akq' size='340' side='right' caption='[[1akq]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br>
		+	<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=1akq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akq RCSB], [http://www.ebi.ac.uk/pdbsum/1akq 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/ak/1akq_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 side chain of aspartate 95 in flavodoxin from Desulfovibrio vulgaris provides the closest negative charge to N(1) of the bound FMN in the protein. Site-directed mutagenesis was used to substitute alanine, asparagine, or glutamate for this amino acid to assess the effect of this charge on the semiquinone/hydroquinone redox potential (E(1)) of the FMN cofactor. The D95A mutation shifts the E(1) redox potential positively by 16 mV, while a negative shift of 23 mV occurs in the oxidized/semiquinone midpoint redox potential (E(2)). The crystal structures of the oxidized and semiquinone forms of this mutant are similar to the corresponding states of the wild-type protein. In contrast to the wild-type protein, a further change in structure occurs in the D95A mutant in the hydroquinone form. The side chain of Y98 flips into an energetically more favorable edge-to-face interaction with the bound FMN. Analysis of the structural changes in the D95A mutant, taking into account electrostatic interactions at the FMN binding site, suggests that the pi-pi electrostatic repulsions have only a minor contribution to the very low E(1) redox potential of the FMN cofactor when bound to apoflavodoxin. Substitution of D95 with glutamate causes only a slight perturbation of the two one-electron redox potentials of the FMN cofactor. The structure of the D95E mutant reveals a large movement of the 60-loop (residues 60-64) away from the flavin in the oxidized structure. Reduction of this mutant to the hydroquinone causes the conformation of the 60-loop to revert back to that occurring in the structures of the wild-type protein. The crystal structures of the D95E mutant imply that electrostatic repulsion between a carboxylate on the side chain at position 95 and the phenol ring of Y98 prevents rotation of the Y98 side chain to a more energetically favorable conformation as occurs in the D95A mutant. Replacement of D95 with asparagine has no effect on E(2) but causes E(1) to change by 45 mV. The D95N mutant failed to crystallize. The K(d) values of the protein FMN complex in all three oxidation-reduction states differ from those of the wild-type complexes. Molecular modeling showed that the conformational energy of the protein changes with the redox state, in qualitative agreement with the observed changes in K(d), and allowed the electrostatic interactions between the FMN and the surrounding groups on the protein to be quantified.

-	~~{{STRUCTURE_1akq\| PDB=1akq \| SCENE= }}~~	+	Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin.,McCarthy AA, Walsh MA, Verma CS, O'Connell DP, Reinhold M, Yalloway GN, D'Arcy D, Higgins TM, Voordouw G, Mayhew SG Biochemistry. 2002 Sep 10;41(36):10950-62. PMID:12206666<ref>PMID:12206666</ref>

-	~~===D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12206666}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1akq]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfovibrio_vulgaris_str~~.~~_hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA].~~	+

	==See Also==		==See Also==
	*[[Flavodoxin\|Flavodoxin]]		*[[Flavodoxin\|Flavodoxin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012206666<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
	[[Category: Higgins, T.]]		[[Category: Higgins, T.]]

OCA at 13:40, 20 October 2012

OCA — Sat, 20 Oct 2012 13:40:23 GMT

←Older revision		Revision as of 13:40, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1akq]] is a 1 chain structure ~~of [[Flavodoxin]]~~ with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA].	+	[[1akq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKQ OCA].

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