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The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans

Nature Structural & Molecular Biology volume 10, pages 285–290 (2003)Cite this article

Abstract

The first crystal structure of a native di-iron center in an iron-storage protein (bacterio)ferritin is reported. The protein, isolated from the anaerobic bacterium Desulfovibrio desulfuricans, has the unique property of having Fe-coproporphyrin III as its heme cofactor. The three-dimensional structure of this bacterioferritin was determined in three distinct catalytic/redox states by X-ray crystallography (at 1.95, 2.05 and 2.35 Å resolution), corresponding to different intermediates of the di-iron ferroxidase site. Conformational changes associated with these intermediates support the idea of a route for iron entry into the protein shell through a pore that passes through the di-iron center. Molecular surface and electrostatic potential calculations also suggest the presence of another ion channel, distant from the channels at the three- and four-fold axes proposed as points of entry for the iron atoms.

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Figure 1: Overall view of the Dd Bfr in structure A.
Figure 2: Stereo view of the electron density averaged over eight independent dimers of the Fe-coproporphyrin III heme cofactor in structure A.
Figure 3: The di-iron center of Dd Bfr.
Figure 4: Views of a Bfr monomer with overlaid molecular surface showing the surface pore that allows access to the di-iron center for structures
Figure 5: Electrostatic potential surfaces of Dd Bfr.

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Acknowledgements

This work was supported by PRAXIS XXI and POCTI grants. We thank the ESRF, Grenoble (France) for the provision of synchrotron radiation and for a grant to S.M.

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Authors and Affiliations

  1. Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, EAN, Apartado 127, Oeiras, 2781-901, Portugal

    Sofia Macedo, Célia V. Romão, Pedro M. Matias, António V. Xavier, Miguel Teixeira, Peter Lindley & Maria A. Carrondo

  2. ESRF, BP-220, Grenoble, F-38043, Cedex, France

    Sofia Macedo, Edward Mitchell & Peter Lindley

  3. Department of Biochemistry, University of Georgia, Athens, 30602, Georgia, USA

    Ming Y. Liu & Jean LeGall

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Macedo, S., Romão, C., Mitchell, E. et al. The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans. Nat Struct Mol Biol 10, 285–290 (2003). https://doi.org/10.1038/nsb909

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