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Alternative metal-binding sites in rubrerythrin

Nature Structural Biology volume 6, pages 308–309 (1999)Cite this article

Rubrerythrin is a dimeric nonheme iron protein isolated from Desulfovibrio vulgaris1. Each subunit contains a rubredoxin-like iron center and a binuclear metal center. A number of enzymatic activities have been associated with the metalloprotein2,3,4,5,6,7,8, but the physiological function of the protein remains unknown.

The ligands for the hexa-coordinate metal at A are the same as in 1RYT except for the substitution of an water or hydroxyl oxygen atom for the μ-oxo bridge in 1RYT. The second metal is located 2.0 Å from the Fe1 site in 1RYT. Four significant changes in the coordination of this metal are the switch of Glu 20 from a bidentate to a monodentate binding mode, the loss of Glu 97 and the μ-oxo bridging atom as ligands and the addition of His 56 as ligand. These changes make this metal tetracoordinate (Fig. 1c). Superposition of 1RYT with our model shows that very small conformational alterations are sufficient to change from one structure to the other.

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Figure 1: a, Difference electron density (|Fo| - |Fc|) for aerobically purified rubrerythrin.

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Acknowledgements

Diffraction data were collected at N.H. Xuong's area detector facility at the university of california, San Diego.

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Authors and Affiliations

  1. Department of Biological Structure and Biomolecular Structure Center, Box 357420

    L.C. Sieker, I. Le Trong, S. Turley & R.E. Stenkamp

  2. University of Washington, Seattle, 98195-7420, Washington

    L.C. Sieker, I. Le Trong, S. Turley & R.E. Stenkamp

  3. C3-168 Molecular Medicine, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, 98109, Washington

    M. Holmes

  4. Physical BioSciences Division, 504 Stanley Hall, E.O. Lawrence Berkeley National Laboratory, Berkeley, 94720, California

    B.D. Santarsiero

  5. Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, 30602-7229, Georgia

    M.-Y. Liu & J. LeGall

  6. Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Apartado 127, Oeiras, 2780, Portugal

    J. LeGall

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  1. L.C. Sieker
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Correspondence to R.E. Stenkamp.

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Sieker, L., Holmes, M., Trong, I. et al. Alternative metal-binding sites in rubrerythrin. Nat Struct Mol Biol 6, 308–309 (1999). https://doi.org/10.1038/7538

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