1yv1: Difference between revisions

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<StructureSection load='1yv1' size='340' side='right'caption='[[1yv1]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='1yv1' size='340' side='right'caption='[[1yv1]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1yv1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1YV1 FirstGlance]. <br>
<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>
</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]] 1.5&#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;'>[[1yux|1yux]], [[1yuz|1yuz]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ngr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1yv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv1 OCA], [http://pdbe.org/1yv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yv1 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/NIGY_DESVH NIGY_DESVH]] Exhibits NADH peroxidase activity (in vitro).  
[https://www.uniprot.org/uniprot/NIGY_DESVH NIGY_DESVH] Exhibits NADH peroxidase activity (in vitro).
== 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=1yv1 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=1yv1 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:15895271<ref>PMID:15895271</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1yv1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Desvh]]
[[Category: Desulfovibrio vulgaris str. Hildenborough]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Iyer, R B]]
[[Category: Iyer RB]]
[[Category: Kurtz, D M]]
[[Category: Kurtz DM]]
[[Category: Lanzilotta, W N]]
[[Category: Lanzilotta WN]]
[[Category: Silaghi-Dumitrescu, R]]
[[Category: Silaghi-Dumitrescu R]]
[[Category: Diiron center]]
[[Category: Electron transfer]]
[[Category: Hemerythrin]]
[[Category: Oxidoreductase]]
[[Category: Peroxidase]]
[[Category: Rubredoxin]]
[[Category: Rubrerythrin]]
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