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Comparison of low oxidoreduction potential cytochrome c 553 from Desulfovibrio vulgaris with the class I cytochrome c family
Author(s) -
Blackledge Martin J.,
Guerlesquin Françoise,
Marion Dominique
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199602)24:2<178::aid-prot5>3.0.co;2-f
Subject(s) - class (philosophy) , computer science , artificial intelligence
The cytochrome c 553 from Desulfovibrio vulgaris (DvH c 553) is of importance in the understanding of the relationship of structure and function of cytochrome c due to its lack of sequence homology with other cytochromes, and its abnormally low oxido‐reduction potential. In evolutionary terms, this protein also represents an important reference point for the understanding of both bacterial and mitochondrial cytochromes c. Using the recently determined nuclear magnetic resonance (NMR) structure of the reduced protein we compare the structural, dynamic, and functional characteristics of DvH c 553 with members of both the mitochondrial and bacterial cytochromes c to characterize the protein in the context of the cytochrome c family, and to understand better the control of oxido‐reduction potential in electron transfer proteins. Despite the low sequence homology, striking structural similarities between this protein and representatives of both eukaryotic [cytochrome c from tuna (tuna c )] and prokaryotic [ Pseudomonas aeruginosa c 551 (Psa c 551)] cytochromes c have been recognized. The previously observed helical core is also found in the DvH c 553. The structural framework and hydrogen bonding network of the DvH c 553 is most similar to that of the tuna c, with the exception of an insertion loop of 24 residues closing the heme pocket and protecting the propionates, which is absent in the DvH c 553. In contrast, the Psa c 551 protects the propionates from the solvent principally by extending the methionine ligand arm. The electrostatic distribution at the recognized encounter surface around the heme in the mitochondrial cytochrome is reproduced in the DvH c 553, and corresponding hydrogen bonding networks, particularly in the vicinity of the heme cleft, exist in both molecules. Thus, although the cytochrome DvH c 553 exhibits higher primary sequence homology to other bacterial cytochromes c , the structural and physical homology is significantly greater with respect to the mitochondrial cytochrome c . The major structural and functional difference is the absence of solvent protection for the heme, differentiating this cytochrome from both reference cytochromes, which have evolved different mechanisms to cover the propionates. This suggests that the abnormal redox potential of the DvH c 553 is linked to the raised accessibility of the heme and supports the theory that redox potential in cytochromes is controlled by heme propionate solvent accessibility.