3ak2: Difference between revisions
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< | ==Superoxide dismutase from Aeropyrum pernix K1, Mn-bound form== | ||
<StructureSection load='3ak2' size='340' side='right'caption='[[3ak2]], [[Resolution|resolution]] 1.35Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ak2]] 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=3AK2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AK2 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3ak2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ak2 OCA], [https://pdbe.org/3ak2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ak2 RCSB], [https://www.ebi.ac.uk/pdbsum/3ak2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ak2 ProSAT]</span></td></tr> | |||
</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;"> | |||
== 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<ref>PMID:21182595</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ak2" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Aeropyrum pernix K1]] | ||
[[ | [[Category: Large Structures]] | ||
[[Category: Nakamura T]] | |||
== | [[Category: Uegaki K]] | ||
< | |||
[[Category: Aeropyrum pernix]] | |||
[[Category: | |||
[[Category: Nakamura | |||
[[Category: Uegaki | |||
Latest revision as of 18:47, 4 October 2023
Superoxide dismutase from Aeropyrum pernix K1, Mn-bound formSuperoxide dismutase from Aeropyrum pernix K1, Mn-bound form
Structural highlights
FunctionSODF_AERPE Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. Publication Abstract from PubMedAeropyrum 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 AlsoReferences
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