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1akv

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[[Image:1akv.gif|left|200px]]<br /><applet load="1akv" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1akv, resolution 2.0&Aring;" />
 
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'''D95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS'''<br />
 
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==Overview==
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==D95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS==
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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.
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<StructureSection load='1akv' size='340' side='right'caption='[[1akv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1akv]] 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=1AKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AKV FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1akv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akv OCA], [https://pdbe.org/1akv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1akv RCSB], [https://www.ebi.ac.uk/pdbsum/1akv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1akv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH] Low-potential electron donor to a number of redox enzymes.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/1akv_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1akv ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1AKV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=FMN:'>FMN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=FMN:Fmn+Co-Factor'>FMN</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKV OCA].
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*[[Flavodoxin 3D structures|Flavodoxin 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12206666 12206666]
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[[Category: Desulfovibrio vulgaris str. Hildenborough]]
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[[Category: Desulfovibrio vulgaris]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Higgins T]]
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[[Category: Higgins, T.]]
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[[Category: Mccarthy A]]
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[[Category: Mccarthy, A.]]
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[[Category: Walsh M]]
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[[Category: Walsh, M.]]
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[[Category: FMN]]
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[[Category: SO4]]
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[[Category: electron transfer]]
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[[Category: electron transport]]
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[[Category: flavodoxin]]
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[[Category: flavoprotein]]
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[[Category: fmn]]
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[[Category: mutant]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:30:48 2008''
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Current revision

D95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS

PDB ID 1akv

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