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Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors

Authors

  • Lim Heo,

    1. Department of Chemistry, Seoul National University, Seoul, Republic of Korea
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  • Yoo-Bok Cho,

    1. School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
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  • Myeong Sup Lee,

    1. Department of Biochemistry, Yonsei University, Seoul, Republic of Korea
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  • Jung-Hye Roe,

    Corresponding author
    1. School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
    • Correspondence to: Chaok Seok, Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea. E-mail: chaok@snu.ac.kr; Jung-Hye Roe, School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-747, Republic of Korea. E-mail: jhroe@snu.ac.kr

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  • Chaok Seok

    Corresponding author
    1. Department of Chemistry, Seoul National University, Seoul, Republic of Korea
    • Correspondence to: Chaok Seok, Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea. E-mail: chaok@snu.ac.kr; Jung-Hye Roe, School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-747, Republic of Korea. E-mail: jhroe@snu.ac.kr

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ABSTRACT

Certain bacterial zinc-containing anti-sigma (ZAS) factors respond sensitively to thiol-induced oxidative stress by undergoing conformational changes, which in turn reduce binding affinities for their cognate sigma factors. This redox sensitivity provides a mechanism for coping with oxidative stress by activating the transcription of antioxidant genes. Not all ZAS proteins are redox-sensitive, but the mechanism of redox sensitivity is not fully understood. Here we propose that alternative zinc-binding sites determine redox sensitivity. To support this proposal, we performed protein modeling and zinc docking on redox-sensitive and redox-insensitive ZAS proteins complexed with their cognate sigma factors. At least one strong alternative zinc-binding pocket was detected for all known redox-sensitive ZAS factors in actinomycetes, while no strong alternative zinc-binding pocket was identified in redox-insensitive ZAS factors, except for one controversial case. This hypothesis of alternative zinc-binding sites can also explain residue-specific contributions to the redox sensitivity of RsrA, a redox-sensing ZAS protein from Streptomyces coelicolor, for which alanine mutagenesis experiments are available. Our results suggest a mechanistic model for redox sensitivity as follows: zinc ion can probabilistically occupy multiple sites in redox-sensitive ZAS proteins, increasing the susceptibility of zinc-coordinating cysteine residues to oxidation. This picture of probabilistic zinc occupation agrees with a previous structure and energy analysis on zinc finger proteins, and thus it may be more widely applicable to other classes of reactive zinc-binding proteins. © 2013 Wiley Periodicals, Inc.

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