Terrance E. Meyer

New perspectives on c-type cytochromes.

Publisher Summary This chapter discusses the various classes of c-type cytochromes, primarily as they occur in nonmitochondrial systems, and their further description as subclasses based on structural relationships observed for purified proteins. The discussion of cytochromes in general is weighted in terms of c-type cytochromes, which present the most examples of readily soluble forms amenable to experiment at the pure protein level. Possible structural interrelationships with membrane-bound forms are considered. Primarily on the basis of amino acid sequences and three-dimensional structures, there are three totally unrelated types of c-type cytochromes, classes I, II, and III. A brief outline of the properties of the classes and subclasses of the c-type cytochromes is presented. The classic problem of structure–function correlation arises in all the classes of prokaryotic c-type cytochromes.

The cytochromes of Chlorobium thiosulfatophilum

Three c-type cytochromes (c-551, c-553, c-555) have been isolated and characterized from a strain of the green photosynthetic bacterium Chlorobium thiosulfatophilum. These cytochromes are atypical when compared to horse heart cytochrome c in many properties, among them: oxidation-reduction potential at pH 7.0 (c-551, 135 mV; c-553, 98 mV; c-555, 145 mV), molecular weight (c-551, 45000–60000; c-553, 50000; c-555, 10000) and isolelectric point (c-551, 6.0; c-553, 6.7). No protoheme was detected in whole cells or cell-free extracts.

Redox potentials of the photosynthetic bacterial cytochromes c2 and the structural bases for variability

The cytochromes c2 of the Rhodospirillaceae show a much greater variation in redox potential and its pH dependence than the mitochondrial cytochromes c that have been studied. It is proposed that the range of redox potential for cytochromes c2 functioning as the immediate electron donor to photo-oxidised bacteriochlorophyll may be 345-395 mV at pH 5. Closely related cytochromes c2 with different redox potentials show patterns of amino acid substitution which are consistent with changes in hydrophobicity near the haem being at least a partial determinant of redox potential. More distantly related cytochromes are difficult to compare because of the large number of amino acid substitutions and the probability that there are subtle changes in overall peptide chain folding. The redox potential versus pH curves can be analysed in terms of either one ionisation in the oxidised form or two in the oxidised form and one in the reduced. The pK in the oxidised form at higher pH values can be correlated with the pK for the disappearance or shift of the near infrared absorption band located near 695 nm. The structural bases of these ionisations are not known but the possible involvement of the haem propionate residues is discussed.

Anomalies in amino acid sequences of small cytochromes c and cytochromes c' from two species of purple photosynthetic bacteria.

MOST species of the Rhodospirillaceae1, the purple nonsulphur photosynthetic bacteria, produce large quantities of cytochrome c2 (ref. 2), a protein which is similar in sequence to mitochondrial cytochrome c3. Many species also produce the high-spin haem protein cytochrome c′ (ref 2). Cytochromes c′ have been identified in Rhodopseudomonas gelatinosa and in Rhodospirillum tenue, but in these organisms the predominant low-spin cytochromes c do not have properties similar to those found for cytochromes c2 (ref. 2). We have now determined the amino acid sequences of the cytochromes c′ and of the predominant low-spin cytochromes c from the two organisms (Fig. 1).

pH dependence of the oxidation-reduction potential of cytochrome c2.

The pH dependence of the spectra and of the oxidation-reduction potential of three cytochromes c2, from Rhodopseudomonas capsulata, Rhodopseudomonas sphaeroides and Rhodomicrobium vannielii, were studied. A single alkaline pK was observed for the spectral changes in all three ferricytochromes. In Rps. capsulata cytochrome c2 this spectroscopic pK corresponds to the pK observed in the dependence of oxidation-reduction potential on pH. For the other two cytochromes the oxidation-reduction potential showed a complex dependency on pH which can be fitted to theoretical curves involving three ionizations. The third ionization corresponds to the ionization observed in the spectroscopic studies but the first two occur without changes in the visible spectra. The possible structural bases for these ionizations are discussed.

Cytochrome c3. A class of electron transfer heme proteins found in both photosynthetic and sulfate-reducing bacteria

Abstract Cytochromes c with absorption spectra and oxidation-reduction potentials very similar to those of Desulfovibrio vulgaris cytochrome c3 were isolated from the photosynthetic bacteria Chloropseudomonas ethylicum, Rhodopseudomonas spheroides and Rps. palustris, as well as from the blue-green alga Anacystis nidulans. Analysis of the highly purified C. ethylicum cytochrome c-551.5 indicates that this protein contains three heme groups per molecule, as compared to Desulfovibrio cytochrome c3, which has four hemes. It is suggested that a special class of cytochromes c be recognized which has absorption spectra and oxidation-reduction potentials similar to those of Desulfovibrio cytochrome c3.

A reassessment of the structure of Paracoccus cytochrome c-550

Abstract An amino acid sequence and a three-dimensional structure of cytochrome c -550 from the facultatively denitrifying aerobic bacterium Paracoccus denitrificans have been reported (Timkovich et al. , 1976; Timkovich & Dickerson, 1976). The amino acid sequence showed considerable similarity to Rhodospirillaceae (purple phototrophic bacterial) cytochrome c 2 , but also had some unexpected features. We have reexamined the amino acid sequence and have found five discrepancies. The molecule contains an additional tryptophan residue, which was not detected in either the 2.5 A crystallographic analysis or the original sequence investigation.

Isolation and properties of rubredoxin from the photosynthetic green sulfur bacteria

Abstract Rubredoxin with properties like those of clostridial rubredoxin has been isolated from two species of green sulfur photosynthetic bacteria, Chlorobium thiosulfatophilum and Choloropseudomonas ethylicum . Rubredoxin was not detected in the several purple sulfur and non-sulfur photosynthetic bacteria tested. No indication of the role of rubredoxin in photosynthetic bacteria is yet apparent.

Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.

The photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein (SHP), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. Similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotrophMethylophilus methylotrophus and the metal reducing bacterium Shewanella putrefaciens. A three-dimensional structure of SHP was derived using the multiple isomorphous replacement phasing method. Besides a model for the oxidized state (to 1.82 Å resolution), models for the reduced state (2.1 Å resolution), the oxidized molecule liganded with cyanide (1.90 Å resolution), and the reduced molecule liganded with nitric oxide (2.20 Å resolution) could be derived. The SHP structure represents a new variation of the class I cytochrome c fold. The oxidized state reveals a novel sixth heme ligand, Asn88, which moves away from the iron upon reduction or when small molecules bind. The distal side of the heme has a striking resemblance to other heme proteins that bind gaseous compounds. In SHP the liberated amide group of Asn88 stabilizes solvent-shielded ligands through a hydrogen bond.

Amino acid sequence of high-redox-potential ferredoxin (HiPIP) isozymes from the extremely halophilic purple phototrophic bacterium, Ectothiorhodospira halophila.

The amino acid sequences of high-redox-potential ferredoxin (HiPIP) isozymes from Ectothiorhodospira halophila have been determined. These are: isozyme I, EPRAEDGHAHDYVNEAADPSHGRYQEGQLCENCAFWGEAVQDGWGRCTHPDFDEVLVKAEGWCSVYAPA S, and isozyme II, GLPDGVEDLPKAEDDHAHDYVNDAADTDHARFQEGQLCENCQFWVDYVNGWGYCQHPDFTDVLVRGEGW CSVYAPA. Isozyme II is the major form of HiPIP produced by the bacterium (65-80%) and is the most acidic of the known HiPIPs. The two isozymes are 72% identical to one another and require only a single residue deletion for alignment. Comparison of these HiPIPs with seven previously determined sequences revealed only 27% average identity. Both E. halophila HiPIP isozymes are likely to be functional since their sequences are equally distant from those of other species. The E. halophila HiPIP sequences show that H-bonding patterns recognized in Chromatium vinosum HiPIP are likely to be conserved and therefore cannot explain the unusually low redox potentials which have been reported.