Tertiary Structure of [2Fe-2S] Ferredoxin from Spirulina platensis Refined at 2.5 Å Resolution: Structural Comparisons of Plant-Type Ferredoxins and an Electrostatic Potential Analysis

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Abstract
The structure of plant-type [2Fe-2S] ferredoxin isolated from Spirulina platensis has been refined using diffraction data to 2.5 Å resolution by alternate cycles of simulated annealing and manual revision of the model. The final R factor is 19.9% for 2,912 reflections with F > 2σF between 8.0 and 2.5 Å resolution. S. platensis ferredoxin, like other plant-type [2Fe-2S] ferredoxins, has a major α-helix flanking a sheet consisting of four β strands. The present refinement revises the conformation of residues 56–71, in which a one-turn helix was identified. Superposition of the Spirulina ferredoxin structure on the structures of other ferredoxins that have been well refined showed structural perturbation at a few residues on the amino and carboxyl termini and the turn between the first and second β-strands. The root-mean-square deviations of the corresponding Cα atoms of the pairs of ferredoxins range from 0.90 to 1.17 Å for all the residues, but from 0.64 to 0.70 Å if the few perturbed residues are excluded. Therefore, it may be concluded that the main-chain foldings of all the plant-type [2Fe-2S] ferredoxins are essentially the same. Electrostatic potential analysis showed that the molecular surface around the cluster is negatively charged, whereas that of the β-sheet of the other side is positively charged. The interaction between ferredoxin and ferredoxin-NADP+ reductase is discussed on the basis of the charge distributions of these molecules and biochemical data