Tài liệu Báo cáo khoa học: Crystal structure of the cambialistic superoxide dismutase from Aeropyrum

Crystal structure of the cambialistic superoxide dismutase

from Aeropyrum pernix K1 – insights into the enzyme

mechanism and stability

Tsutomu Nakamura1

, Kasumi Torikai1,2, Koichi Uegaki1

, Junji Morita2

, Kodai Machida3,4,

Atsushi Suzuki5 and Yasushi Kawata3,4

1 National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan

2 Department of Food Science and Nutrition, Faculty of Human Life and Science, Doshisha Women’s College of Liberal Arts, Kyoto, Japan

3 Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Japan

4 Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science,

Tottori University, Japan

5 Power Train Material Engineering Division, Toyota Motor Corporation, Aichi, Japan

Keywords

Aeropyrum pernix; cambialistic; metal

coordination; stability; superoxide dismutase

Correspondence

T. Nakamura, National Institute of Advanced

Industrial Science and Technology, 1-8-31

Midorigaoka, Ikeda, Osaka 563-8577, Japan

Fax: +81 72 751 8370

Tel: +81 72 751 9272

E-mail: [email protected]

(Received 2 August 2010, revised 28

October 2010, accepted 2 December 2010)

doi:10.1111/j.1742-4658.2010.07977.x

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. per￾nix in the apo, Mn-bound and Fe-bound forms were determined at resolu￾tions 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 bind￾ing 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 sta￾bility than the enzyme from T. thermophilus. This suggests that dominant

ion pairs make A. pernix superoxide dismutase tolerant to organic media.

Database

Structural data have been deposited in the Protein Data Bank under the accession numbers

3AK1 (apo-form), 3AK2 (Mn-bound form) and 3AK3 (Fe-bound form)

Structured digital abstract

l MINT-8075688: Superoxide dismutase (uniprotkb:Q9Y8H8) and Superoxide dismutase

(uniprotkb:Q9Y8H8) bind (MI:0407) by cosedimentation in solution (MI:0028)

l MINT-8075667: Superoxide dismutase (uniprotkb:Q9Y8H8) and Superoxide dismutase

(uniprotkb:Q9Y8H8) bind (MI:0407) by x-ray crystallography (MI:0114)

l MINT-8075678: Superoxide dismutase (uniprotkb:Q9Y8H8) and Superoxide dismutase

(uniprotkb:Q9Y8H8) bind (MI:0407) by molecular sieving (MI:0071)

Abbreviations

ApeSOD, superoxide dismutase from Aeropyrum pernix; SOD, superoxide dismutase; TthSOD, superoxide dismutase from

Thermus thermophilus.

598 FEBS Journal 278 (2011) 598–609 ª 2010 The Authors Journal compilation ª 2010 FEBS