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<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
<table><tr><td colspan='2'>[[1lko]] 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=1LKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
</td></tr><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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.63&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lkm|1lkm]], [[1lkp|1lkp]]</div></td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [https://pdbe.org/1lko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [https://www.ebi.ac.uk/pdbsum/1lko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [https://pdbe.org/1lko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [https://www.ebi.ac.uk/pdbsum/1lko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1lko ConSurf].
</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=1lko ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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--&gt;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.
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:12175244<ref>PMID:12175244</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1lko" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 29579]]
[[Category: Desulfovibrio vulgaris]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Jin, S]]
[[Category: Jin S]]
[[Category: Kurtz, D M]]
[[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: Diiron]]
[[Category: Electron transport]]
[[Category: Four-helix bundle]]
[[Category: Reduced form]]
[[Category: Rubredoxin-like]]
[[Category: Rubrerythrin]]

Latest revision as of 07:33, 14 February 2024

Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form

1lko, resolution 1.63Å

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