Hybrid-Cluster Protein (HCP) from Desulfovibrio vulgaris (Hildenborough) at 1.6 Å Resolution

• Published in: Biochemistry (Easton) 2000-12, Vol.39 (49), p.15044-15054
• Main Authors: Cooper, S. J, Garner, C. D, Hagen, W. R, Lindley, P. F, Bailey, S
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacterial Proteins - chemistry; Crystallography, X-Ray; Desulfovibrio vulgaris; Fourier Analysis; Iron-Sulfur Proteins - chemistry; Models, Molecular; Molecular Sequence Data; Protein Structure, Tertiary; Sequence Homology, Amino Acid; Synchrotrons
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi001483m

The three-dimensional structure of the hybrid cluster protein from Desulfovibrio vulgaris (Hildenborough) has been determined at 1.6 Å resolution using synchrotron X-ray radiation. The protein can be divided into three domains:  an N-terminal mainly α-helical domain and two similar domains comprising a central β-sheet flanked by α-helices. The protein contains two 4Fe clusters with an edge-to-edge distance of 10.9 Å. 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 μ-sulfido bridges, two μ2-oxo bridges, and a further disordered bridging ligand. Anomalous differences in data collected at 1.488 Å and close to the iron edge at 1.743 Å 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.