3AK1

Superoxide dismutase from Aeropyrum pernix K1, apo-form

Summary for 3AK1

• Entry DOI: 10.2210/pdb3ak1/pdb
• Related: 3AK2 3AK3
• Descriptor: Superoxide dismutase [Mn/Fe], 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: superoxide dismutase, cambialistic, oxidoreductase
• Biological source: Aeropyrum pernix
• Total number of polymer chains: 4
• Total formula weight: 100050.87

Authors

Nakamura, T.,Uegaki, K. (deposition date: 2010-06-30, release date: 2011-02-02, Last modification date: 2023-11-01)

Primary citation

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., 278:598-609, 2011

PubMed Abstract: 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 Å, 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.

PubMed: 21182595
DOI: 10.1111/j.1742-4658.2010.07977.x

Experimental method

X-RAY DIFFRACTION (1.57 Å)