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| | ==Superoxide dismutase from Aeropyrum pernix K1, apo-form== | | ==Superoxide dismutase from Aeropyrum pernix K1, apo-form== |
| - | <StructureSection load='3ak1' size='340' side='right' caption='[[3ak1]], [[Resolution|resolution]] 1.57Å' scene=''> | + | <StructureSection load='3ak1' size='340' side='right'caption='[[3ak1]], [[Resolution|resolution]] 1.57Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ak1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AK1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ak1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AK1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.57Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ak2|3ak2]], [[3ak3|3ak3]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE0741 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 Aeropyrum pernix])</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=3ak1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ak1 OCA], [https://pdbe.org/3ak1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ak1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ak1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ak1 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ak1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ak1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ak1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ak1 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SODF_AERPE SODF_AERPE] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3ak1" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Superoxide Dismutase|Superoxide Dismutase]] | + | *[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aeropyrum pernix]] | + | [[Category: Aeropyrum pernix K1]] |
| - | [[Category: Superoxide dismutase]] | + | [[Category: Large Structures]] |
| - | [[Category: Nakamura, T.]] | + | [[Category: Nakamura T]] |
| - | [[Category: Uegaki, K.]] | + | [[Category: Uegaki K]] |
| - | [[Category: Cambialistic]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Superoxide dismutase]]
| + | |
| Structural highlights
Function
SODF_AERPE Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
Publication Abstract from PubMed
Aeropyrum pernix K1, an aerobic hyperthermophilic archaeon, produces a cambialistic superoxide dismutase that is active in the presence of either of Mn or Fe. The crystal structures of the superoxide dismutase from A. pernix in the apo, Mn-bound and Fe-bound forms were determined at resolutions of 1.56, 1.35 and 1.48 A, respectively. The overall structure consisted of a compact homotetramer. Analytical ultracentrifugation was used to confirm the tetrameric association in solution. In the Mn-bound form, the metal was in trigonal bipyramidal coordination with five ligands: four side chain atoms and a water oxygen. One aspartate and two histidine side chains ligated to the central metal on the equatorial plane. In the Fe-bound form, an additional water molecule was observed between the two histidines on the equatorial plane and the metal was in octahedral coordination with six ligands. The additional water occupied the postulated superoxide binding site. The thermal stability of the enzyme was compared with superoxide dismutase from Thermus thermophilus, a thermophilic bacterium, which contained fewer ion pairs. In aqueous solution, the stabilities of the two enzymes were almost identical but, when the solution contained ethylene glycol or ethanol, the A. pernix enzyme had significantly higher thermal stability than the enzyme from T. thermophilus. This suggests that dominant ion pairs make A. pernix superoxide dismutase tolerant to organic media. Structured digital abstract * MINT-8075688: Superoxide dismutase (uniprotkb:Q9Y8H8) and Superoxide dismutase (uniprotkb:Q9Y8H8) bind (MI:0407) by cosedimentation in solution (MI:0028) * MINT-8075667: Superoxide dismutase (uniprotkb:Q9Y8H8) and Superoxide dismutase (uniprotkb:Q9Y8H8) bind (MI:0407) by x-ray crystallography (MI:0114) * MINT-8075678: Superoxide dismutase (uniprotkb:Q9Y8H8) and Superoxide dismutase (uniprotkb:Q9Y8H8) bind (MI:0407) by molecular sieving (MI:0071).
Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability.,Nakamura T, Torikai K, Uegaki K, Morita J, Machida K, Suzuki A, Kawata Y FEBS J. 2010 Dec 7. doi: 10.1111/j.1742-4658.2010.07977.x. PMID:21182595[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nakamura T, Torikai K, Uegaki K, Morita J, Machida K, Suzuki A, Kawata Y. Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability. FEBS J. 2010 Dec 7. doi: 10.1111/j.1742-4658.2010.07977.x. PMID:21182595 doi:10.1111/j.1742-4658.2010.07977.x
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