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1yv1

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(New page: 200px<br /><applet load="1yv1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yv1, resolution 1.50&Aring;" /> '''Fully reduced state ...)
Current revision (09:00, 14 February 2024) (edit) (undo)
 
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[[Image:1yv1.gif|left|200px]]<br /><applet load="1yv1" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yv1, resolution 1.50&Aring;" />
 
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'''Fully reduced state of nigerythrin (all ferrous)'''<br />
 
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==Overview==
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==Fully reduced state of nigerythrin (all ferrous)==
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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='1yv1' size='340' side='right'caption='[[1yv1]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1yv1]] 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=1YV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YV1 FirstGlance]. <br>
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1YV1 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 FE2 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YV1 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]] 1.5&#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=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=1yv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv1 OCA], [https://pdbe.org/1yv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yv1 RCSB], [https://www.ebi.ac.uk/pdbsum/1yv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv1 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: FE2]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/1yv1_consurf.spt"</scriptWhenChecked>
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[[Category: diiron center]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: electron transfer]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: hemerythrin]]
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</jmolCheckbox>
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[[Category: peroxidase]]
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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=1yv1 ConSurf].
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[[Category: rubredoxin]]
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<div style="clear:both"></div>
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[[Category: rubrerythrin]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:04:17 2007''
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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

Fully reduced state of nigerythrin (all ferrous)

PDB ID 1yv1

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