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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

  • Germaine Sainz
  • Jean Jakoncic
  • Larry C. Sieker
  • Vivian Stojanoff
  • Nukri Sanishvili
  • Marcel Asso
  • Patrick Bertrand
  • Jean Armengaud
  • Yves Jouanneau
Original Paper

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.

Keywords

Ferredoxin Crystal structure Iron–sulfur cluster Redox potential Conformational changes 

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

Notes

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.

Supplementary material

775_2005_69_MOESM1_ESM.pdf (314 kb)
Supplementary material

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Copyright information

© SBIC 2006

Authors and Affiliations

  • Germaine Sainz
    • 1
  • Jean Jakoncic
    • 1
    • 2
  • Larry C. Sieker
    • 3
  • Vivian Stojanoff
    • 1
    • 2
  • Nukri Sanishvili
    • 4
  • Marcel Asso
    • 5
  • Patrick Bertrand
    • 5
  • Jean Armengaud
    • 6
    • 7
  • Yves Jouanneau
    • 6
  1. 1.European Synchrotron Radiation FacilityGrenoble Cedex 9France
  2. 2.Brookhaven National LaboratoryNational Synchrotron Light SourceUptonUSA
  3. 3.Department of Biological StructureUniversity of WashingtonSeattleUSA
  4. 4.Structural Biology Center/Midwest Center for Structural GenomicsArgonne National Laboratory ArgonneUSA
  5. 5.Laboratoire de Bioénergétique et Ingénierie des ProtéinesUPR 9036 CNRSMarseille Cedex 20France
  6. 6.Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, CNRS UMR 5092, Département Réponse et Dynamique CellulairesCEA-GrenobleGrenoble Cedex 9France
  7. 7.CEA-Valrho, DSV-DIEP-SBTNBagnols-sur-Cèze CedexFrance

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