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| - | [[Image:1lkp.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form, azide adduct== |
| - | |PDB= 1lkp |SIZE=350|CAPTION= <scene name='initialview01'>1lkp</scene>, resolution 1.64Å
| + | <StructureSection load='1lkp' size='340' side='right'caption='[[1lkp]], [[Resolution|resolution]] 1.64Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene> | + | <table><tr><td colspan='2'>[[1lkp]] is a 1 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=1LKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKP FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.64Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkp OCA], [https://pdbe.org/1lkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkp RCSB], [https://www.ebi.ac.uk/pdbsum/1lkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkp ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1lkm|1LKM]], [[1lko|1LKO]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkp OCA], [http://www.ebi.ac.uk/pdbsum/1lkp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1lkp RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity). |
| - | | + | == Evolutionary Conservation == |
| - | '''Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form, azide adduct'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lkp_consurf.spt"</scriptWhenChecked> |
| - | Rubrerythrin (Rbr) is a 44-kDa homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [Fe(SCys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. The diiron site structure resembles those found in O2-activating diiron enzymes. However, Rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). The diferrous site in all-ferrous Rbr (Rbr(red)) shows a much greater reactivity with H2O2 than does the diferric site in all-ferric Rbr (Rbr(ox)), but only the latter structure has been reported. Here we report the X-ray crystal structures of the recombinant Rbr(red) from the sulfate reducing bacterium, Desulfovibrio vulgaris, as well as its azide adduct (Rbr(red)N3). We have also redetermined the structure of Rbr(ox) to a higher resolution than previously reported. The structural differences between Rbr(ox) and Rbr(red) are localized entirely at the diiron site. The most striking structural change upon reduction of the diferric to the diferrous site of Rbr is a 1.8-A movement of one iron away from a unique glutamate carboxylate ligand and toward a trans-disposed histidine side chain, which replaces the glutamate as a ligand. This movement increases the inter-iron distance from 3.3 to 4 A. Rbr(red)N(3) shows this same iron movement and His-->Glu ligand replacement relative to Rbr(ox), and, in addition, an azide coordinated to the diiron site in a cis mu-1,3 fashion, replacing two solvent ligands in Rbr(red). Relative to those in O2-activating enzymes, the bridging carboxylate ligation of the Rbr diiron site is less flexible upon diferric/diferrous interconversion. The diferrous site is also much more rigid, symmetrical, and solvent-exposed than those in O2-activating enzymes. On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1LKP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKP OCA].
| + | </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=1lkp ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase., Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC, J Am Chem Soc. 2002 Aug 21;124(33):9845-55. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12175244 12175244]
| + | </StructureSection> |
| | [[Category: Desulfovibrio vulgaris]] | | [[Category: Desulfovibrio vulgaris]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Jin, S.]] | + | [[Category: Jin S]] |
| - | [[Category: Jr., D M.Kurtz.]] | + | [[Category: Kurtz Jr DM]] |
| - | [[Category: Liu, Z J.]] | + | [[Category: Liu ZJ]] |
| - | [[Category: Rose, J.]] | + | [[Category: Rose J]] |
| - | [[Category: Wang, B C.]] | + | [[Category: Wang BC]] |
| - | [[Category: azide adduct]]
| + | |
| - | [[Category: diiron]]
| + | |
| - | [[Category: four-helix bundle]]
| + | |
| - | [[Category: reduced form]]
| + | |
| - | [[Category: rubredoxin-like]]
| + | |
| - | [[Category: rubrerythrin]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:03:57 2008''
| + | |
