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Structure of a [2Fe–2S] ferredoxin from Rhodobacter capsulatus likely involved in Fe–S cluster biogenesis and conformational changes observed upon reduction

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Abstract

FdVI from Rhodobacter capsulatus is structurally related to a group of [2Fe–2S] ferredoxins involved in iron–sulfur cluster biosynthesis. Comparative genomics suggested that FdVI and orthologs found in α-Proteobacteria are involved in this process. Here, the crystal structure of FdVI has been determined for both the oxidized and the reduced protein. The [2Fe–2S] cluster lies 6 Å below the protein surface in a hydrophobic pocket without access to the solvent. This particular cluster environment might explain why the FdVI midpoint redox potential (−306 mV at pH 8.0) did not show temperature or ionic strength dependence. Besides the four cysteines that bind the cluster, FdVI features an extra cysteine which is located close to the S1 atom of the cluster and is oriented in a position such that its thiol group points towards the solvent. Upon reduction, the general fold of the polypeptide chain was almost unchanged. The [2Fe–2S] cluster underwent a conformational change from a planar to a distorted lozenge. In the vicinity of the cluster, the side chain of Met24 was rotated by 180°, bringing its S atom within hydrogen-bonding distance of the S2 atom of the cluster. The reduced molecule also featured a higher content of bound water molecules, and more extensive hydrogen-bonding networks compared with the oxidized molecule. The unique conformational changes observed in FdVI upon reduction are discussed in the light of structural studies performed on related ferredoxins.

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Abbreviations

Adx:

Adrenodoxin

AnFd:

Anabaena PCC7119 ferredoxin

EPR:

Electron paramagnetic resonance

Fd:

Ferredoxin

Fdx:

Ferredoxin from Escherichia coli

MAD:

Multiple anomalous dispersion

Pdx:

Putidaredoxin

rms:

Root mean square

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Acknowledgements

We thank Christine Meyer for helping in the purification of FdVI. We are indebted to Emile Duée and Eric Fanchon for helpful discussion. Thanks to D. Bourgeois, X. Vernede, R. Morales and J. Fontecilla for helpful advice and for giving us access to the facilities which allowed us to obtain and analyze reduced crystals of FdVI. We wish to thank Valerie Biou, Janet Smith and Andrew Thompson for valuable suggestions and support. Funding for this project was provided by the Centre National de la Recherche Scientifique, the Commissariat à l’Energie Atomique, the European Synchrotron Radiation Facility and the NIGMS under agreement Y1 GM-0080.

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Author notes

  1. Jean Jakoncic

    Present address: Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY, 11973, USA

Authors and Affiliations

  1. European Synchrotron Radiation Facility, BP 220, 38054, Grenoble Cedex 9, France

    Germaine Sainz, Jean Jakoncic & Vivian Stojanoff

  2. Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY, 11973, USA

    Vivian Stojanoff

  3. Department of Biological Structure, University of Washington, Seattle, WA, USA

    Larry C. Sieker

  4. Structural Biology Center/Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, 60439, USA

    Nukri Sanishvili

  5. Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036 CNRS, 13402, Marseille Cedex 20, France

    Marcel Asso & Patrick Bertrand

  6. Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, CNRS UMR 5092, Département Réponse et Dynamique Cellulaires, CEA-Grenoble, 38054, Grenoble Cedex 9, France

    Jean Armengaud & Yves Jouanneau

  7. CEA-Valrho, DSV-DIEP-SBTN, BP 171, 30207, Bagnols-sur-Cèze Cedex, France

    Jean Armengaud

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  1. Germaine Sainz
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Corresponding author

Correspondence to Yves Jouanneau.

Additional information

Germaine Sainz and Jean Jakoncic contributed equally to this work.

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Sainz, G., Jakoncic, J., Sieker, L.C. et al. Structure of a [2Fe–2S] ferredoxin from Rhodobacter capsulatus likely involved in Fe–S cluster biogenesis and conformational changes observed upon reduction. J Biol Inorg Chem 11, 235–246 (2006). https://doi.org/10.1007/s00775-005-0069-2

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  • DOI: https://doi.org/10.1007/s00775-005-0069-2

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