The three-dimensional structure of the hybrid cluster protein from Desulfovibrio vulgaris (Hildenborough) has been determined at 1.6 A resolution using synchrotron X-ray radiation. The protein can be divided into three domains: an N-terminal mainly alpha-helical domain and two similar domains comprising a central beta-sheet flanked by alpha-helices. The protein contains two 4Fe clusters with an edge-to-edge distance of 10.9 A. Four cysteine residues at the N-terminus of the protein are ligands to the iron atoms of a conventional [4Fe-4S] cubane cluster. The second cluster has an unusual asymmetric structure and has been named the hybrid cluster to reflect the variety of protein ligands, namely two mu-sulfido bridges, two mu(2)-oxo bridges, and a further disordered bridging ligand. Anomalous differences in data collected at 1.488 A and close to the iron edge at 1.743 A have been used to confirm the identity of the metal and sulfur atoms. The hybrid cluster is buried in the center of the protein, but is accessible through a large hydrophobic cavity that runs the length of domain 3. Hydrophobic channels have previously been identified as access routes to the active centers in redox enzymes with gaseous substrates. The hybrid cluster is also accessible by a hydrophilic channel. The [4Fe-4S] cubane cluster is close to an indentation on the surface of the protein and can also be approached on the opposite side by a long solvent channel. At the present time, neither the significance of these channels nor, indeed, the function of the hybrid cluster protein is known.

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Crystals of the prismane protein from Desulfovibrio vulgaris (Hildenborough) containing a putative [6Fe-6S] cluster have been obtained and X-ray data collected to a resolution of 1.7 A using synchrotron radiation. The unit cell is orthorhombic with a = 64.1, b = 65.1 and c = 154.1 A, space group P2(1)2(1)2(1) (No. 19). The unit cell will readily accommodate four molecules of molecular weight 60 kDa with a corresponding solvent content of approximately 48%.

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Genes encoding hybrid cluster proteins (HCPs) are widespread among bacterial and archaeal species and are found within the nitrate assimilation gene region. The crystal structure of HCP from Desulfovibrio vulgaris (Hildenborough) reveals two 4Fe clusters with an edge‐to‐edge distance of 10.9 Å. The first cluster is a conventional [4Fe4S] cubane cluster. The second cluster has an unusual asymmetric structure and has been named the hybrid cluster to reflect the variety of protein ligands. Both the hybrid cluster and the cubane cluster give rise to unusual EPR signals and the hybrid cluster has four stable oxidation states. The physiological role of HCP is currently uncertain, although HCP from Rhodobacter capsulatus catalyzes hydroxylamine reduction, suggesting a role in the assimilation of hydroxylamine.

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