title: Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 A resolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis.
abstract: The structure of plant-type [2Fe-2S] ferredoxin isolated from Spirulina platensis has been refined using diffraction data to 2.5 A 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 > 2 sigma F between 8.0 and 2.5 A resolution. S. platensis ferredoxin, like other plant-type [2Fe-2S] ferredoxins, has a major alpha-helix flanking a sheet consisting of four beta 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 beta-strands. The root-mean-square deviations of the corresponding C alpha atoms of the pairs of ferredoxins range from 0.90 to 1.17 A for all the residues, but from 0.64 to 0.70 A 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 beta-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.
authors.affiliation: Department of Biology, Faculty of Science, Osaka University.
authors.forename: K
authors.initials: K
authors.lastname: Fukuyama
authors.forename: N
authors.initials: N
authors.lastname: Ueki
authors.forename: H
authors.initials: H
authors.lastname: Nakamura
authors.forename: T
authors.initials: T
authors.lastname: Tsukihara
authors.forename: H
authors.initials: H
authors.lastname: Matsubara
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D018360:Crystallography, X-Ray; D000458:Cyanobacteria / Q000737:chemistry*; D004563:Electrochemistry; D005287:Ferredoxin-NADP Reductase / Q000737:chemistry / Q000378:metabolism; D005288:Ferredoxins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry; D017434:Protein Structure, Tertiary
chemical_list: D001426:Bacterial Proteins; D005288:Ferredoxins; D010940:Plant Proteins; D005287:Ferredoxin-NADP Reductase