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2dsx

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(New page: 200px<br /><applet load="2dsx" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dsx, resolution 0.68&Aring;" /> '''Crystal structure of...)
Current revision (13:48, 13 March 2024) (edit) (undo)
 
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[[Image:2dsx.gif|left|200px]]<br /><applet load="2dsx" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2dsx, resolution 0.68&Aring;" />
 
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'''Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution'''<br />
 
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==Overview==
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==Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution==
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Rubredoxin (D.g. Rd) is a small non-heme iron-sulfur protein shown to, function as a redox coupling protein from the sulfate reducing bacteria, Desulfovibrio gigas. The protein is generally purified from anaerobic, bacteria in which it is thought to be involved in electron transfer or, exchange processes. Rd transfers an electron to oxygen to form water as, part of a unique electron transfer chain, composed by NADH:rubredoxin, oxidoreductase (NRO), rubredoxin and rubredoxin:oxygen oxidoreductase, (ROO) in D.g. The crystal structure of D.g. Rd has been determined by, means of both a Fe single-wavelength anomalous dispersion (SAD) signal and, the direct method, and refined to an ultra-high 0.68 A resolution, using, X-ray from a synchrotron. Rd contains one iron atom bound in a tetrahedral, coordination by the sulfur atoms of four cysteinyl residues. Hydrophobic, and pi-pi interactions maintain the internal Rd folding. Multiple, conformations of the iron-sulfur cluster and amino acid residues are, observed and indicate its unique mechanism of electron transfer. Several, hydrogen bonds, including N-H...SG of the iron-sulfur, are revealed, clearly in maps of electron density. Abundant waters bound to C-O peptides, of residues Val8, Cys9, Gly10, Ala38, and Gly43, which may be involved in, electron transfer. This ultrahigh-resolution structure allows us to study, in great detail the relationship between structure and function of, rubredoxin, such as salt bridges, hydrogen bonds, water structures, cysteine ligands, iron-sulfur cluster, and distributions of electron, density among activity sites. For the first time, this information will, provide a clear role for this protein in a strict anaerobic bacterium.
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<StructureSection load='2dsx' size='340' side='right'caption='[[2dsx]], [[Resolution|resolution]] 0.68&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2dsx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DSX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DSX 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]] 0.68&#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=FE:FE+(III)+ION'>FE</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=2dsx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dsx OCA], [https://pdbe.org/2dsx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dsx RCSB], [https://www.ebi.ac.uk/pdbsum/2dsx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dsx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RUBR_MEGGA RUBR_MEGGA] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.
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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/ds/2dsx_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=2dsx 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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2DSX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas] with FE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DSX OCA].
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*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
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*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
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==Reference==
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__TOC__
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Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution., Chen CJ, Lin YH, Huang YC, Liu MY, Biochem Biophys Res Commun. 2006 Oct 13;349(1):79-90. Epub 2006 Aug 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16930541 16930541]
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</StructureSection>
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[[Category: Desulfovibrio gigas]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Megalodesulfovibrio gigas]]
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[[Category: Chen, C.J.]]
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[[Category: Chen C-J]]
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[[Category: Huang, Y.C.]]
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[[Category: Huang Y-C]]
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[[Category: Lin, Y.H.]]
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[[Category: Lin Y-H]]
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[[Category: Liu, M.Y.]]
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[[Category: Liu M-Y]]
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[[Category: FE]]
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[[Category: desulfovibrio gigas]]
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[[Category: redox]]
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[[Category: rubredoxin]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:45:58 2007''
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Current revision

Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution

PDB ID 2dsx

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