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1yuz

From Proteopedia

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[[Image:1yuz.gif|left|200px]]<br /><applet load="1yuz" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yuz, resolution 1.40&Aring;" />
 
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'''Partially Reduced State of Nigerythrin'''<br />
 
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==Overview==
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==Partially Reduced State of Nigerythrin==
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High-resolution crystal structures of Desulfovibrio vulgaris nigerythrin (DvNgr), a member of the rubrerythrin (Rbr) family, demonstrate an approximately 2-A movement of one iron (Fe1) of the diiron site from a carboxylate to a histidine ligand upon conversion of the mixed-valent ([Fe2(II),Fe1(III)]) to diferrous states, even at cryogenic temperatures. This Glu&lt;--&gt;His ligand "toggling" of one iron, which also occurs in DvRbr, thus, appears to be a characteristic feature of Rbr-type diiron sites. Unique features of DvNgr revealed by these structures include redox-induced flipping of a peptide carbonyl that reversibly forms a hydrogen bond to the histidine ligand to Fe1 of the diiron site, an intra-subunit proximal orientation of the rubredoxin-(Rub)-like and diiron domains, and an electron transfer pathway consisting of six covalent and two hydrogen bonds connecting the Rub-like iron with Fe2 of the diiron site. This pathway can account for DvNgr's relatively rapid peroxidase turnover. The characteristic combination of iron sites together with the redox-dependent iron toggling between protein ligands can account for the selectivity of Rbrs for hydrogen peroxide over dioxygen.
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<StructureSection load='1yuz' size='340' side='right'caption='[[1yuz]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1yuz]] is a 2 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=1YUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YUZ FirstGlance]. <br>
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1YUZ 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=FE:'>FE</scene> and <scene name='pdbligand=FE2:'>FE2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YUZ OCA].
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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]] 1.4&#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>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
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==Reference==
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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=1yuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yuz OCA], [https://pdbe.org/1yuz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yuz RCSB], [https://www.ebi.ac.uk/pdbsum/1yuz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yuz ProSAT]</span></td></tr>
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High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins., Iyer RB, Silaghi-Dumitrescu R, Kurtz DM Jr, Lanzilotta WN, J Biol Inorg Chem. 2005 Jun;10(4):407-16. Epub 2005 May 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15895271 15895271]
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</table>
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[[Category: Desulfovibrio vulgaris]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/NIGY_DESVH NIGY_DESVH] Exhibits NADH peroxidase activity (in vitro).
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[[Category: Iyer, R B.]]
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== Evolutionary Conservation ==
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[[Category: Kurtz, D M.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Lanzilotta, W N.]]
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Check<jmol>
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[[Category: Silaghi-Dumitrescu, R.]]
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<jmolCheckbox>
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[[Category: FE]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yu/1yuz_consurf.spt"</scriptWhenChecked>
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[[Category: FE2]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: diiron center]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: electron transfer]]
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</jmolCheckbox>
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[[Category: hemerythrin]]
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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=1yuz ConSurf].
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[[Category: rubredoxin]]
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<div style="clear:both"></div>
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[[Category: rubrythrin]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:09:25 2008''
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[[Category: Desulfovibrio vulgaris str. Hildenborough]]
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[[Category: Large Structures]]
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[[Category: Iyer RB]]
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[[Category: Kurtz DM]]
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[[Category: Lanzilotta WN]]
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[[Category: Silaghi-Dumitrescu R]]

Current revision

Partially Reduced State of Nigerythrin

PDB ID 1yuz

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