Examination of protein sequence homologies: IV. Twenty-seven bacterial ferredoxins

Abstract

Sequence homologies of 27 bacterial ferredoxins were examined using a computer program that quantitatively evaluates extent of similarity as a correlation coefficient. The results of a similarity search among the sequences demonstrated that the basal sequence consists of a pair of extremely similar segments of 26 amino acids connected by a three-amino acid group. The segment pairs, which would have arisen from gene duplication, are termed the first and second units. Because of the gene duplication, the connector sequence appears to have been introduced as a structurally important chain reversal. Each of the two units contains four cysteine residues, which are inserted one by one among seven, two, two, three, and eight amino acid alignments, respectively. The bacterial ferredoxins were categorized with regard to basal constitution as follows: group 1, in which both units closely conform to the basal structure; group 2, in which the second unit is modified in a characteristic manner among members; group 3, in which the first unit is modified in a characteristic manner, while the conforming second unit is accompanied by a long accessory sequence; group 4, in which there are modifications before and/or after the units, of which the respective central domains remain nearly intact; and group 5, where only the former of two Fe:S cluster ligation sets of four cysteines is estimated to remain intact, whereas the latter set is extremely modified. It is noteworthy that throughout all bacterial ferredoxins, one of two cysteine sets never fails to be completely intact and, moreover, the connector of three amino acids also exists intact. Based on this grouping and on the correspondences among the groups, average correlation coefficients among all members were computed, and the respective evolutionary relationships were examined. The results supported the proposition that transposition had occurred in the Azotobacter-type ferredoxins of group 3.

Identification and analysis of the dissimilatory nitrous oxide reduction genes, nosRZDFY, of Rhizobium meliloti

“…A short segment of the sequence including the first cluster showed identity in database searches with several 4Fe-4S bacterial ferredoxins. A match was seen to the last three of the four cysteines in the ferredoxin consensus sequence, CX 2 CX 2 CX 3 C(P/E/G) (32), while the first two cysteines were separated by three instead of two residues (Fig. 5).…”

Crystal structure of the 2[4Fe‐4S] ferredoxin from Chromatium vinosum: Evolutionary and mechanistic inferences for [3/4Fe‐4S] ferredoxins

“…These structural differences are supportive of the divergent evolution of the various ferredoxin families beginning with the duplication of an ancestral gene, as is recognized most easily in short, clostridial type ferredoxins (Otaka & Ooi, 1987). From the presumably oldest sequences retaining an almost perfect internal symmetry as in CaFd (Figs.…”

Selective interaction of ferricyanide with cluster I of Clostridium pasteurianum 2[Fe4S4] ferredoxin

“…Possible physiological roles of the iron ion loss/ uptake mechanisms, resulting in activity control and modulation, have been suggested for such proteins. Comparing the primary sequences of these Fe,!& proteins containing a labile metal we observe that the first three iron ligands (Cys, Y = Cys or Asp, and Cys) are always comprised in a sequence of the type cys-x-x-Y-x-x-cys whereas the fourth ligand (Cys) lies in a different portion of the protein [35,36]. Upon conversion of a Fe& cluster into the corresponding Fe& cluster it is usually the central Y residue (Cys or Asp) of the above sequence to be detached.…”