High-Resolution Structure of the Soluble, Respiratory-Type Rieske Protein fromThermus thermophilus:  Analysis and Comparison

Abstract

The structure of the soluble Rieske protein from Thermus thermophilus has been determined at a resolution of 1.3 A at pH 8.5 using multiwavelength anomalous dispersion (MAD) techniques. This is the first report of a Rieske protein from a menaquinone-utilizing organism. The structure shows an overall fold similar to previously reported Rieske proteins. A novel feature of this crystal form appears to be a shared hydrogen between the His-134 imidazole ring ligated to Fe2 of the [2Fe-2S] cluster and its symmetry partner, His-134', one being formally an imidazolate anion, Fe2-(His-134)N(epsilon)(-)...H-N(epsilon')(His-134')-Fe2', in which crystallographic C(2) axes pass equidistant between N(epsilon)...N(epsilon') and normal to the line defined by N(epsilon)...N(epsilon'). This provides evidence for a stable, oxidized cluster with a His(-) ligand and lends support to a previously proposed mechanism of coupled proton and electron transfer. A detailed comparison of the Thermus Rieske protein with six other Rieske and Rieske-type proteins indicates: (a) The cluster binding domain is tightly conserved. (b) The 3-D structure of the 10 beta-strand fold is conserved, even among the most divergent proteins. (c) There is an approximately linear relation between acid-pH redox potential and number of H-bonds to the cluster. (d) These proteins have two faces, one points into the larger complex (bc(1), b(6)f, or other), is involved in the proton coupled electron transfer function, and is highly conserved. The second is oriented toward the solvent and shows wide variation in charge, sequence, length, hydrophobicity, and secondary elements in the loops that connect the beta-sheets.

X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc1: Comparison with its Mitochondrial and Chloroplast Counterparts

“…Clearly, the core structure of the FeS protein, including both the base and the cluster binding folds, is well conserved and the extra residues are accomodated in a small number of insertions in linkers between secondary structure elements. As pointed out previously (Hunsicker-Wang et al 2003), the modified inserts are on the side of the extrinsic domain facing away from the rest of the complex, while the side contacting the complex is highly conserved.…”

“…Finally, although the sequence from Thermus thermophilus is too dissimilar to be reliably aligned by sequence alone, its high-resolution structure (1NYK) (Hunsicker-Wang et al 2003) indicates that this linker is shorter than that in the mitochondrial proteins, and superposing the structures shows nothing in the region around the DxxR 3-10 helix.…”

Modifications of Protein Environment of the [2Fe-2S] Cluster of the bc1 Complex

“…Structures of the bc 1 complexes from many dif-ferent species from chicken to photosynthetic bacteria have now been resolved (3-8) so we could study the homology of the structures of ISP from various species. The strong homology between sequences of the [2Fe-2S] binding domains suggests a minimal structural deviation among species (8,29,54). In this study, we have taken advantage of the facility for molecular engineering and for functional characterization in R. sphaeroides to explore detailed aspects of the structure-function interface.…”

Rational Design of a Mononuclear Metal Site into the Archaeal Rieske-type Protein Scaffold

“…The "two cysteines plus two histidines"-type coordination pattern commonly observed in the Rieske-type proteins/domains (17,43,44) might have been preferred in the modular evolution process of an early Rieske-type protein scaffold, as a consequence of the geometric tolerance of the metal-binding loops for the [2Fe-2S] cluster insertion and/or assembly. The ligand exchange and metal-and/or cluster-type conversion might have been key evolutionary events from an archetypal mononuclear metalloprotein module toward a modern, high potential Rieske protein subunit of the respiratory complexes III, in which one of two histidyl ligands plays crucial electron/ proton transfer roles in the quinol-oxidizing Q o -site catalysis (16,18).…”