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Journal of Biochemistry Advance Access published online on October 9, 2009
Journal of Biochemistry, doi:10.1093/jb/mvp154
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© The authors 2009. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Crystal Structure of Peroxiredoxin from Aeropyrum pernix K1 Complexed with its Substrate, Hydrogen Peroxide

Tsutomu Nakamura1,*,{dagger}, Yuji Kado2,*, Takafumi Yamaguchi2,{ddagger}, Hiroyoshi Matsumura2, Kazuhiko Ishikawa1 and Tsuyoshi Inoue2

1National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577 and 2Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan

{dagger} Corresponding author: Tsutomu Nakamura, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan. E-mail: nakamura-t{at}aist.go.jp, TEL: +81 72 751 9272 , FAX: +81 72 751 8370.

Received June 10, 2009; Accepted September 3, 2009


  Abstract

Peroxiredoxin reduces hydrogen peroxide and alkyl peroxides to water and corresponding alcohols, respectively. The reaction is dependent on a peroxidatic cysteine, whose sulfur atom nucleophilically attacks one of the oxygen atoms of the peroxide substrate. In spite of the many structural studies that have been carried out on this reaction, the tertiary structure of the hydrogen peroxide-bound form of peroxiredoxin has not been elucidated. In this paper, we report the crystal structure of peroxiredoxin from Aeropyrum pernix K1 in the peroxide-bound form. The conformation of the polypeptide chain is the same as that in the reduced apo-form. The hydrogen peroxide molecule is in close contact with the peroxidatic Cys50 and the neighboring Thr47 and Arg126 side chain atoms, as well as with the main chain nitrogen atoms of Val49 and Cys50. Bound peroxide was also observed in the mutant C50S, in which the peroxidatic cysteine was replaced by serine. Therefore, the sulfur atom of the peroxidatic cysteine is not essential for peroxide binding, although it enhances the binding affinity. Hydrogen peroxide binds to the protein so that it fills the active site pocket. This study provides insight into the early stage of the peroxiredoxin reaction.

Key Words: Aeropyrum pernix K1, hydrogen peroxide, peroxidatic cysteine, peroxiredoxin, thioredoxin peroxidase

* These two authors equally contributed to this work.

{ddagger} Present address: Dia/-Nitric Co. Ltd., Tsurumi, Yokohama, Kanagawa 230-0053, Japan


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