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NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c 556

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Abstract

The structure of oxidized Rhodopseudomonas palustris cytochrome c 556 has been modeled after that of high-spin cytochrome c′ from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. The two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. In order to validate this modeled structure, several structural restraints were obtained by performing a restricted set of NMR experiments, without performing a complete assignment of the protein signals. The aim was to exploit the special restraints arising from the paramagnetism of the metal ion. A total of 43 residual-dipolar-coupling and 74 pseudocontact-shift restraints, which together sampled all regions of the protein, were used in conjunction with over 40 routinely obtained NOE distance restraints. A calculation procedure was undertaken combining the program MODELLER and the solution structure determination program PARAMAGNETIC DYANA, which includes paramagnetism-based restraints. The directions and magnitude of the magnetic susceptibility anisotropy tensor were also calculated. The approach readily provides useful results, especially for paramagnetic metalloproteins of moderate to large dimensions.

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Acknowledgements

This work was supported by Murst ex 40%, Italy, the European Union, contracts HPRI-CT-2001-00147 and QLG2-CT-1999-01003, CNR, Italy, contract 99.00950.CT03, and the United States Department of Energy (grant no. DE-FG03-02ER15359 to Caltech).

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Authors and Affiliations

  1. CERM and Department of Chemistry, University of Florence, via L. Sacconi 6, 50019 , Sesto Fiorentino, Italy

    Ivano Bertini

  2. Beckman Institute, California Institute of Technology, Pasadena, CA , 91125, USA

    Jasmin Faraone-Mennella, Harry B. Gray & Jay R. Winkler

  3. CERM and Department of Agricultural Biotechnology, University of Florence, p.le delle Cascine 28, 50144 , Florence, Italy

    Claudio Luchinat & Giacomo Parigi

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  1. Ivano Bertini
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  2. Jasmin Faraone-Mennella
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  3. Harry B. Gray
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  4. Claudio Luchinat
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  5. Giacomo Parigi
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  6. Jay R. Winkler
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Correspondence to Ivano Bertini.

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Bertini, I., Faraone-Mennella, J., Gray, H.B. et al. NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c 556 . J Biol Inorg Chem 9, 224–230 (2004). https://doi.org/10.1007/s00775-003-0511-2

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  • DOI: https://doi.org/10.1007/s00775-003-0511-2

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