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J. Biol. Chem., Vol. 277, Issue 37, 34499-34507, September 13, 2002

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High Resolution Crystal Structures of the Wild Type and Cys-55  Ser and Cys-59  Ser Variants of the Thioredoxin-like [2Fe-2S] Ferredoxin from Aquifex aeolicus^*

Andrew P. Yeh, Xavier I. Ambroggio^§, Susana L. A. Andrade^¶, Oliver Einsle^¶, Claire Chatelet, Jacques Meyer^**, and Douglas C. Rees^¶**

From the  Division of Chemistry and Chemical Engineering, the ^§ Division of Biology, and the ^¶ Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125 and the  Département de Biologie Moléculaire et Structurale, Commissariat à l'Energie Atomique, Grenoble F-38054, France

The [2Fe-2S] ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like polypeptide fold that is distinct from other [2Fe-2S] ferredoxins. Crystal structures of the Cys-55  Ser (C55S) and Cys-59  Ser (C59S) variants of this protein have been determined to 1.25 Å and 1.05 Å resolution, respectively, whereas the resolution of the wild type (WT) has been extended to 1.5 Å. The improved WT structure provides a detailed description of the [2Fe-2S] cluster, including two features that have not been noted previously in any [2Fe-2S] cluster-containing protein, namely, pronounced distortions in the cysteine coordination to the cluster and a C-H-S hydrogen bond between cluster ligands Cys-55 and Cys-9. These features may contribute to the unusual electronic and magnetic properties of the [2Fe-2S] clusters in WT and variants of this ferredoxin. The structures of the two variants of Fd4, in which single cysteine ligands to the [2Fe-2S] cluster are replaced by serine, establish the metric details of serine-ligated Fe-S active sites with unprecedented accuracy. Both the cluster and its surrounding protein matrix change in subtle ways to accommodate this ligand substitution, particularly in terms of distortions of the Fe₂S₂ inorganic core from planarity and displacements of the polypeptide chain. These high resolution structures illustrate how the interactions between polypeptide chains and Fe-S active sites reflect combinations of flexibility and rigidity on the part of both partners; these themes are also evident in more complex systems, as exemplified by changes associated with serine ligation of the nitrogenase P cluster.

The atomic coordinates and the structure factors (code 1M2A, 1M2B and 1M2D) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

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