1bu5

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(New page: 200px<br /><applet load="1bu5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bu5, resolution 1.83&Aring;" /> '''X-RAY CRYSTAL STRUCT...)
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[[Image:1bu5.gif|left|200px]]<br /><applet load="1bu5" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bu5, resolution 1.83&Aring;" />
 
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'''X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX'''<br />
 
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==Overview==
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==X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX==
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The apoprotein of flavodoxin from Desulfovibrio vulgaris forms a complex, with riboflavin. The ability to bind riboflavin distinguishes this, flavodoxin from other short-chain flavodoxins which require the phosphate, of FMN for flavin binding. The redox potential of the, semiquinone/hydroquinone couple of the bound riboflavin is 180 mV less, negative than the corresponding complex with FMN. To elucidate the binding, of riboflavin, the complex has been crystallized and the crystal structure, solved by molecular replacement using native flavodoxin as a search model, to a resolution of 0.183 nm. Compared to the FMN complex, the, hydrogen-bonding network at the isoalloxazine sub-site of the riboflavin, complex is severely disrupted by movement of the loop residues Ser58-Ile64, (60-loop) which contact the isoalloxazine by over 0.35 nm, and by a small, displacement of the isoalloxazine moiety. The 60-loop movement away from, the flavin increases the solvent exposure of the flavin-binding site. The, conformation of the site at which 5'-phosphate of FMN normally binds is, similar in the two complexes, but in the riboflavin complex a sulphate or, phosphate ion from the crystallization buffer occupies the space. This, causes small structural perturbations in the phosphate-binding site. The, flexibility of the 60-loop in D. vulgaris flavodoxin appears to be a, contributing factor to the binding of riboflavin by the apoprotein, and a, feature that distinguishes the protein from other 'short chain', flavodoxins. In the absence of the terminal phosphate group, free movement, at the 5'-OH group of the ribityl chain can occur. Thus, the 5'-phosphate, of FMN secures the cofactor at the binding site and positions it, optimally. The structural changes which occur in the 60-loop in the, riboflavin complex probably account for most of the positive shift that is, observed in the midpoint potential of the semiquinone/hydroquinone couple, of the riboflavin complex compared to that of the FMN complex.
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<StructureSection load='1bu5' size='340' side='right'caption='[[1bu5]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bu5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BU5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BU5 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]] 1.83&#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=RBF:RIBOFLAVIN'>RBF</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=1bu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bu5 OCA], [https://pdbe.org/1bu5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bu5 RCSB], [https://www.ebi.ac.uk/pdbsum/1bu5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bu5 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/bu/1bu5_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=1bu5 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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1BU5 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 SO4 and RBF as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BU5 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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X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex., Walsh MA, McCarthy A, O'Farrell PA, McArdle P, Cunningham PD, Mayhew SG, Higgins TM, Eur J Biochem. 1998 Dec 1;258(2):362-71. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9874201 9874201]
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[[Category: Desulfovibrio vulgaris]]
[[Category: Desulfovibrio vulgaris]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cunningham, P.D.]]
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[[Category: Cunningham PD]]
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[[Category: Farrell, P.A.O.]]
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[[Category: Higgins TM]]
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[[Category: Higgins, T.M.]]
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[[Category: Mayhew SG]]
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[[Category: Mayhew, S.G.]]
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[[Category: Mccardle P]]
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[[Category: Mccardle, P.]]
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[[Category: Mccarthy A]]
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[[Category: Mccarthy, A.]]
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[[Category: O'Farrell PA]]
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[[Category: Walsh, M.A.]]
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[[Category: Walsh MA]]
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[[Category: RBF]]
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[[Category: SO4]]
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[[Category: electron transport]]
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[[Category: flavoprotein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:55:25 2007''
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Current revision

X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX

PDB ID 1bu5

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