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Extremophiles

, Volume 20, Issue 2, pp 177–186 | Cite as

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

  • Yuki Hamajima
  • Takayuki Nagae
  • Nobuhisa Watanabe
  • Eiji Ohmae
  • Yasuyuki Kato-Yamada
  • Chiaki KatoEmail author
Original Paper

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.

Keywords

Deep-sea enzyme High pressure Isopropylmalate dehydrogenase Molecular adaptation Water penetration 

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

Notes

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).

Supplementary material

792_2016_811_MOESM1_ESM.docx (184 kb)
Supplementary material 1 (DOCX 184 kb)

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Copyright information

© Springer Japan 2016

Authors and Affiliations

  • Yuki Hamajima
    • 1
    • 2
  • Takayuki Nagae
    • 3
  • Nobuhisa Watanabe
    • 3
    • 4
  • Eiji Ohmae
    • 5
  • Yasuyuki Kato-Yamada
    • 2
  • Chiaki Kato
    • 1
    Email author
  1. 1.Department of Marine Biodiversity ResearchJapan Agency for Marine-Earth Science and TechnologyYokosukaJapan
  2. 2.Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
  3. 3.Synchrotron Radiation Research CenterNagoya UniversityNagoyaJapan
  4. 4.Department of Biotechnology, Graduate School of EngineeringNagoya UniversityNagoyaJapan
  5. 5.Department of Mathematical and Life Sciences, Graduate School of ScienceHiroshima UniversityHiroshimaJapan

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