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Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers

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Abstract

Isocitrate dehydrogenase from Archaeoglobus fulgidus (AfIDH) has an apparent melting temperature (T m) of 98.5°C. To identify the structural features involved in thermal stabilization of AfIDH, the structure was solved to 2.5 Å resolution. AfIDH was strikingly similar to mesophilic IDH from Escherichia coli (EcIDH) and displayed almost the same number of ion pairs and ionic networks. However, two unique inter-domain networks were present in AfIDH; one three-membered ionic network between the large and the small domain and one four-membered ionic network between the clasp and the small domain. The latter ionic network was presumably reduced in size when the clasp domain of AfIDH was swapped with that of EcIDH and the T m decreased by 18°C. Contrarily, EcIDH was only stabilized by 4°C by the clasp domain of AfIDH, a result probably due to the introduction of a unique inter-subunit aromatic cluster in AfIDH that may strengthen the dimeric interface in this enzyme. A unique aromatic cluster was identified close to the N-terminus of AfIDH that could provide additional stabilization of this region. Common and unique heat adaptive traits of AfIDH with those recently observed for hyperthermophilic IDH from Aeropyrum pernix (ApIDH) and Thermotoga maritima (TmIDH) are discussed herein.

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Abbreviations

IDH:

Isocitrate dehydrogenase

GDH:

Glutamate dehydrogenase

ApIDH:

Aeropyrum pernix IDH

EcIDH:

Escherichia coli IDH

BsIDH:

Bacillus subtilis IDH

TmIDH:

Thermotoga maritima IDH

AfIDH:

Archaeoglobus fulgidus IDH

PfIDH:

Pyrococcus furiosus IDH

T m :

Melting temperature

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Acknowledgments

This work was supported by the Norwegian Research Council (Project no. 153774/420). The Norwegian Structural Biology Centre (NorStruct) is supported by the national Functional Genomics Programme (FUGE) of the Research Council of Norway. Provision of beamtime at the Swiss Light Source is gratefully acknowledged. We are grateful to Prof. Aurora Martinez, Department of Biomedicine, University of Bergen, for access to her laboratory facilities and expertise in use of differential scanning calorimetry. The excellent laboratory skills of Lisbeth Glærum and Marit Steine Madsen are also much appreciated.

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Authors and Affiliations

  1. Department of Biology, University of Bergen, PO Box 7800, Jahnebakken 5, 5020, Bergen, Norway

    Runar Stokke, Nils Kåre Birkeland & Ida Helene Steen

  2. Center for Structural Biochemistry, Department of Biosciences and Nutrition at Novum, Karolinska Institutet, 141 57, Huddinge, Sweden

    Mikael Karlström & Rudolf Ladenstein

  3. The Norwegian Structural Biology Centre (NorStruct), University of Tromsø, 9037, Tromso, Norway

    Nannan Yang & Ingar Leiros

Authors
  1. Runar Stokke
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  2. Mikael Karlström
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  3. Nannan Yang
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  4. Ingar Leiros
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  5. Rudolf Ladenstein
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  6. Nils Kåre Birkeland
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  7. Ida Helene Steen
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Correspondence to Ida Helene Steen.

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Communicated by G. Antranikian.

Enzyme EC number: (EC 1.1.1.42)

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Stokke, R., Karlström, M., Yang, N. et al. Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers. Extremophiles 11, 481–493 (2007). https://doi.org/10.1007/s00792-006-0060-z

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  • DOI: https://doi.org/10.1007/s00792-006-0060-z

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