3ak3

From Proteopedia

Superoxide dismutase from Aeropyrum pernix K1, Fe-bound form

PDB ID 3ak3

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Structural highlights

3ak3 is a 4 chain structure with sequence from Aeropyrum pernix K1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.48Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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