3f7k

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[[Image:3f7k.png|left|200px]]
 
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==X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex==
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The line below this paragraph, containing "STRUCTURE_3f7k", creates the "Structure Box" on the page.
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<StructureSection load='3f7k' size='340' side='right'caption='[[3f7k]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3f7k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alvinella_pompejana Alvinella pompejana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F7K FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.35&#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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3f7k| PDB=3f7k | SCENE= }}
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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=3f7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f7k OCA], [https://pdbe.org/3f7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f7k RCSB], [https://www.ebi.ac.uk/pdbsum/3f7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f7k ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/B6CHW7_9ANNE B6CHW7_9ANNE] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.[RuleBase:RU000393]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/3f7k_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3f7k ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. Alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees C, with spikes up to 84 degrees C. Here, we used Cu,Zn superoxide dismutase (SOD) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability by supplying better stable mammalian homologs for structural biology and other biophysical characterizations than those from prokaryotic thermophiles. Identification, cloning, characterization, X-ray scattering (small-angle X-ray scattering, SAXS), and crystal structure determinations show that A. pompejana SOD (ApSOD) is superstable, homologous, and informative. SAXS solution analyses identify the human-like ApSOD dimer. The crystal structure shows the active site at 0.99 A resolution plus anchoring interaction motifs in loops and termini accounting for enhanced stability of ApSOD versus human SOD. Such stabilizing features may reduce movements that promote inappropriate intermolecular interactions, such as amyloid-like filaments found in SOD mutants causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. ApSOD further provides the structure of a long-sought SOD product complex at 1.35 A resolution, suggesting a unified inner-sphere mechanism for catalysis involving metal ion movement. Notably, this proposed mechanism resolves apparent paradoxes regarding electron transfer. These results extend knowledge of SOD stability and catalysis and suggest that the eukaryote A. pompejana provides macromolecules highly similar to those from humans, but with enhanced stability more suitable for scientific and medical applications.
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===X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex===
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Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.,Shin DS, Didonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA J Mol Biol. 2009 Feb 6;385(5):1534-55. Epub 2008 Nov 25. PMID:19063897<ref>PMID:19063897</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_19063897}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3f7k" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19063897 is the PubMed ID number.
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{{ABSTRACT_PUBMED_19063897}}
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==About this Structure==
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[[3f7k]] is a 1 chain structure of [[Superoxide Dismutase]] with sequence from [http://en.wikipedia.org/wiki/Alvinella_pompejana Alvinella pompejana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F7K OCA].
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==See Also==
==See Also==
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*[[Superoxide Dismutase]]
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*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:19063897</ref><references group="xtra"/>
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__TOC__
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[[Category: Alvinella pompejana]]
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</StructureSection>
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[[Category: Superoxide dismutase]]
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[[Category: Barondeau, D P.]]
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[[Category: DiDonato, M.]]
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[[Category: Getzoff, E D.]]
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[[Category: Shin, D S.]]
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[[Category: Tainer, J A.]]
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[[Category: Al]]
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[[Category: Alvinella pompejana]]
[[Category: Alvinella pompejana]]
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[[Category: Amyloid filament]]
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[[Category: Large Structures]]
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[[Category: Amyotrophic lateral sclerosis]]
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[[Category: Barondeau DP]]
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[[Category: Eukaryotic thermophile]]
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[[Category: DiDonato M]]
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[[Category: Fal]]
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[[Category: Getzoff ED]]
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[[Category: Greek key beta-barrel]]
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[[Category: Shin DS]]
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[[Category: Hydrogen peroxide product complex]]
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[[Category: Tainer JA]]
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[[Category: Lou gehrig's disease]]
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[[Category: Pompeii worm]]
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[[Category: Superoxide dismutase]]
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[[Category: Thermostable protein]]
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Current revision

X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

PDB ID 3f7k

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