Around cysteine residues

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. 

Cluster 1 is a conventional [4Fe-4S] cubane cluster bound near the N-terminus of the molecule as shown in Fig. 13. Within the cluster the Fe-S bonds range from 2.26 to 2.39 A. The cluster is linked to the protein by four cysteine residues with Fe-S distances ranging from 2.21 to 2.35 A, but the distribution of the cysteine residues along the polypeptide chain contrasts markedly with that found, for example, in the ferredoxins as indicated in Section II,B,4 [also see, for example, 41) and references therein]. In the Fepr protein all four cysteine residues (Cys 3, 6, 15, and 21) originate from the N-terminus of the molecule, and the fold of the polypeptide chain in this region is such that it wraps itself tightly around the cluster, yet keeps it near the surface of the molecule. In such a position the cluster is ideally placed to participate in one-electron transfer reactions with other molecules. 

Another group of related electron carriers, the high-potential iron proteins (HIPIP) contain four labile sulfur and four iron atoms per peptide chain 261-266 X-ray studies showed that the 86-residue polypeptide chain of the HIPIP of Chromatium is wrapped around a single iron-sulfur cluster which contains the side chains of four cysteine residues plus the four iron and four sulfur atoms (Fig. 16-15D)261 This kind of cluster is referred to as [4Fe-4S], or as Fe4S4. Each cysteine sulfur is attached to one atom of Fe, with the four iron atoms forming an irregular tetrahedron with an Fe-Fe... 

The protein sequence data in Table 2 show that the cysteine residues in all the proteins occur in identical positions (18, 39, 44, 47, 77) in the sequence. Thus, the ligand field produced by the cysteinyl-sulfur atoms is not likely to be different among these proteins unless there is a difference in protein conformation which causes a displacement in one or more of the cysteinyl sulfur atoms. Note that a displacement of any cysteinyl sulfur atom in the model in Fig. 15 results in rhombic distortion at the iron to which it is ligated. Since, according to the spin-coupled model, this rhombic distortion will manifest itself in the difference between gx and gx for a particular protein, the EPR data in Table 1 provide a measure of the rhombic distortion around the ferrous iron in the reduced proteins. In particular, the g-values of adrenodoxin are axially symmetric while the g-values of spinach ferredoxin show a rhombic distortion. Thus, the observation of Kimura et al. (168) that adrenodoxin and spinach ferredoxin have different protein conformations is consistent with the prediction of the above model. 

A hydrophobic environment around the iron site has been found to exist on the inside of many globular proteins. In the case of HiPIP, an Fe4S4 is buried in the hydrophobic cavity of the protein. The local structure within 5.5 A of the core shows the situation more clearly, as shown in Fig. 16 (53). Especially noticeable here are the Trp side chains, which originate from a characteristic peptide sequence of Trp-Cys or Trp-Cys-Ala at the coordinating cysteine residues. We have examined the effect of Trp by preparation and spectroscopic and electrochemical measurements of its Fe4S4 complexes. 

Fig. 14. X-ray crystal structure of full-length yeast CCS [pdb code Iqup (Lamb et al., 1999)]. (a) One monomer of yCCS is in light gray and the other is in dark gray. The cysteine residues of the MXCXXC motif in domain 1 are labeled and form a disulfide bond in each subunit. Amino acid side chains that are important in the formation of the positive patch at the dimer interface (Arg-188 and Arg-217) and the solvent-exposed Trp-183 residues of loop 6 at the center of this patch are shown in ball-and-stick representation. Domain 3 is not visible in the crystal structure (see text), (b) Stereo view of the image in (a) rotated 90° in the horizontal plane of the page and then 90° counterclockwise around an axis perpendicular to the page. The side chains that form the putative ySODl interaction surface are represented as ball-and-stick. The cysteine residues of the domain 1 MXCXXC motif are also represented in ball-and-stick.

The protease family may be conveniently classified according to their activities and functional groups (cf. Polgar, 1989 for a review). The serine and cystein (or thiol) proteases are endopeptidases that have a reactive serine and cystein residue, respectively, and pH optima around neutrality. Aspartyl (or acid) proteases are also endopeptidases that have catalytically important carboxylate side chains and work optimally at low pH values. At last, zinc proteases are metalloenzymes that function at neutral pH. Many proteases are small monomer enzymes with molecular weights between 15 and 35 kD, readily amenable to kinetic and structural study, this is why they are among the best studied enzymes. The role of electrostatic effects in the catalytic action of these enzymes has been also studied by several authors, and will be considered below. 

The chemokine (CK) subfamily of cytokines with a general conformation of an open-face p-sandwich with a C-terminai a-helical segment, divided into three major subgroups based on the amino acid sequence around the conserved cysteine residues. 

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