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Pressure adaptation of 3-isopropylmalate dehydrogenase from an extremely piezophilic bacterium is attributed to a single amino acid substitution

Extremophiles volume 20, pages 177–186 (2016)Cite this article

Abstract

3-Isopropylmalate dehydrogenase (IPMDH) from the extreme piezophile Shewanella benthica (SbIPMDH) is more pressure-tolerant than that from the atmospheric pressure-adapted Shewanella oneidensis (SoIPMDH). To understand the molecular mechanisms of this pressure tolerance, we analyzed mutated enzymes. The results indicate that only a single mutation at position 266, corresponding to Ala (SbIPMDH) and Ser (SoIPMDH), essentially affects activity under higher-pressure conditions. Structural analyses of SoIPMDH suggests that penetration of three water molecules into the cleft around Ser266 under high-pressure conditions could reduce the activity of the wild-type enzyme; however, no water molecule is observed in the Ala266 mutant.

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Abbreviations

DHFR:

Dihydrofolate reductase

EcDHFR:

DHFR from Escherichia coli

HPPX:

High-pressure protein crystallography

IPM:

Threo-3-isopropylmalate

IPMDH:

3-isopropylmalate dehydrogenase

NAD:

Nicotinamide adenine dinucleotide

RMSD:

Root-mean-square deviation

SbIPMDH:

IPMDH from Shewanella benthica DB21MT-2

SoIPMDH:

IPMDH from Shewanella oneidensis MR-1

TtIPMDH:

IPMDH from Thermus thermophiles

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Acknowledgments

We thank the late Prof. Takeo Imai, Rikkyo University, for the directions of this study. This work was supported partially by Grants-in-Aid for Exploratory Research (25450121, 21657027, and 24570186), the Strategic Research Foundation Grant-aided Project for Private Universities (S1201003) from the Ministry of Education, Culture, Sports, Science and Technology, Japan, and Rikkyo University Special Fund for Research 2014. The synchrotron radiation experiments were performed at AR-NW12A of Photon Factory (Proposal Nos. 2012G648 and 2014G566) and BL41XU of SPring-8 (Proposal No. 2012A1242). The experiments at SPring8 were approved by the Japan Synchrotron Radiation Research Institute (JASRI).

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    Authors and Affiliations

    1. Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan

      Yuki Hamajima & Chiaki Kato

    2. Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan

      Yuki Hamajima & Yasuyuki Kato-Yamada

    3. Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chigusa-ku, Nagoya, Aichi, 464-8603, Japan

      Takayuki Nagae & Nobuhisa Watanabe

    4. Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chigusa-ku, Nagoya, Aichi, 464-8603, Japan

      Nobuhisa Watanabe

    5. Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8511, Japan

      Eiji Ohmae

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    1. Yuki Hamajima
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    Correspondence to Chiaki Kato.

    Additional information

    Communicated by H. Atomi.

    Y. Hamajima and T. Nagae contributed equally to this work.

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    Hamajima, Y., Nagae, T., Watanabe, N. et al. Pressure adaptation of 3-isopropylmalate dehydrogenase from an extremely piezophilic bacterium is attributed to a single amino acid substitution. Extremophiles 20, 177–186 (2016). https://doi.org/10.1007/s00792-016-0811-4

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