Rieske-type protein

Only a few residues show more than 75% sequence identity, including four glycine residues, a proline residue at the beginning of the Pro loop, and a phenylalanine residue in a position corresponding to the conserved residue Tyr 165 of the bovine heart Rieske protein. However, structure prediction and sequence comparison with Rieske proteins from bci complexes suggests that the fold will be very similar in all Rieske-type ferredoxins, as in the other Rieske or Rieske-type proteins (see Section III,B,1). 

In the Rieske proteins from bci or b f complexes, loops (34-/35 and (36-/37 both contain an additional cysteine residue (Cys 144 and Cys 160 in the ISF and Cys 112 and Cys 127 in RFS) these cysteines form a disulfide bridge connecting the two loops (Fig. 3b). These cysteines are not present in the sequences of Rieske-type proteins, that is, in neither NDO nor Rieske-type ferredoxins. In Rieske proteins, the disulfide bridge appears to be important for the stabilization of the fold around the cluster as the two loops are not shielded by other parts of the protein in NDO, the Rieske cluster is stabilized without a disulfide bridge since it is completely buried by surrounding a and (3 subunits. 

Early mutational studies of the Rieske protein from 6ci complexes have been performed with the intention of identifying the ligands of the Rieske cluster. These studies have shown that the four conserved cysteine residues as well as the two conserved histidine residues are essential for the insertion of the [2Fe-2S] cluster (44, 45). Small amounts of a Rieske cluster with altered properties were obtained in Rhodobacter capsulatus when the second cysteine in the cluster binding loop II (Cys 155, corresponding to Cys 160 in the bovine ISF) was replaced by serine (45). The fact that all four cysteine residues are essential in Rieske clusters from be complexes, but that only two cysteines are conserved in Rieske-type clusters, led to the suggestion that the Rieske protein may contain a disulfide bridge the disulfide bridge was finally shown to exist in the X-ray structure (9). 

When the second-site revertants were segregated from the original mutations, the bci complexes carrying a single mutation in the linker region of the Rieske protein had steady-state activities of 70-100% of wild-type levels and cytochrome b reduction rates that were approximately half that of the wild type. In all these mutants, the redox potential of the Rieske cluster was increased by about 70 mV compared to the wild type (51). Since the mutations are in residues that are in the flexible linker, at least 27 A away from the cluster, it is extremely unlikely that any of the mutations would have a direct effect on the redox potential of the cluster that would be observed in the water-soluble fragments. However, the mutations in the flexible linker will affect the mobility of the Rieske protein. Therefore, the effect of the mutations described is due to the interaction between the positional state of the Rieske protein and its electrochemical properties (i.e., the redox potential of the cluster). 

Extinction Coefficients and Ellipticities of the Rieske Protein from Bovine Heart bc Complex (ISF) and of the Rieske-Type Ferredoxin from Benzene Dioxygenase (FiIbed)... 

X-ray absorption spectroscopy has been performed on the isolated Rieske protein from bovine heart mitochondrial bc complex 69) as well as on the Rieske-type cluster in Burkholderia cepacia phthalate dioxygenase (PDO) (72). The analysis performed by Powers et al. 69) was significantly hampered by the fact that the presence of two histidine ligands was not fully recognized therefore, only the results obtained with the dioxygenase where the mononuclear iron has been depleted will be considered here. Table VII gives a comparison of the distances obtained from the fit of the EXAFS spectra assuming an idealized Rieske model and of the distances in the crystal structures... 

Fig. 14. Plot of the g values g,g ) and of the average g value g vs rhombicity (UJ of (a) wild type (open symbol) and variant forms (closed symbols) of the Rieske protein in yeast bci complex where the residues Ser 183 and Tyr 185 forming hydrogen bonds into the cluster have been replaced by site-directed mutagenesis [Denke et al. (35) Merbitz-Zahradnik, T. Link, T. A., manuscript in preparation] and of (b) the Rieske cluster in membranes of Rhodobacter capsulatus in different redox states of the quinone pool and with inhibitors added [data from Ding et al. (79)]. The solid lines represent linear fits to the data points the dashed lines reproduce the fits to the g values of all Rieske and Rieske-type proteins shown in Fig. 13.

The use of direct electrochemical methods (cyclic voltammetry Pig. 17) has enabled us to measure the thermodynamic parameters of isolated water-soluble fragments of the Rieske proteins of various bci complexes (Table XII)). (55, 92). The values determined for the standard reaction entropy, AS°, for both the mitochondrial and the bacterial Rieske fragments are similar to values obtained for water-soluble cytochromes they are more negative than values measured for other electron transfer proteins (93). Large negative values of AS° have been correlated with a less exposed metal site (93). However, this is opposite to what is observed in Rieske proteins, since the cluster appears to be less exposed in Rieske-type ferredoxins that show less negative values of AS° (see Section V,B). 

NDO can be classified as class III dioxygenase the electron transfer chain involves a Rieske-type ferredoxin. Electrons enter NDO through the Rieske-type cluster of the dioxygenase. Kauppi et al. (11) have suggested that the binding site of NDO for the ferredoxin involves the 6 strands 10 and 12 of the Rieske domain as well as residues from the catalytic domain that form a depression in the protein surface close to Cys 101, which is a ligand of the Rieske cluster. In Rieske proteins from be complexes, access to this side of the cluster is blocked by an acidic surface residue (Asp 152 in the ISF, Glu 120 in RFS). 

Since their discovery, Rieske proteins have been the object of numerous studies aimed at gaining insight into the molecular basis of their unique properties. These studies not only have shed light on Rieske and Rieske-type clusters, but also have contributed to the understanding of iron sulfur proteins in general. 

X-ray structures of mitochondrial 6ci complexes from three different sources (113, 124, 125) have found the b- and c-type hemes at roughly identical positions, whereas the Rieske protein was seen in different places as a function of crystal space group and presence or absence of inhibitors of the enzyme. This fact was interpreted to suggest a long-range conformational movement of the Rieske protein during turnover of the complex. The range of observed positions of the Rieske protein indicated that the soluble domain can move like a... 

C) cuboidal three-iron-four-sulfide [Fe3-S4] clusters—stable oxidation states are 0 and + 1 and (D) cubane four-iron-four-sulfide [Fe4-S4] clusters—stable oxidation states are + 1 and +2 for ferredoxin-type clusters and +2 and +3 for HIPIP clusters. Electrons can be delocalized, such that the valences of individual iron atoms lie between ferrous and ferric forms. Low-molecular-weight proteins containing the first and the last three types are referred to as rubredoxins (Rd) and ferredoxins (Fd), respectively. The protein ligands are frequently Cys residues, but a number of others are found, notably His, which replaces two of the thiol ligands in the [Fe2-S2] Rieske proteins. In addition to these, discrete Rd... 

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