Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms

Systematic distortion of [4Fe-4S] cluster in the protein

Keiichi Fukuyama, Toshihiro Okada, Yoshimitsu Kakuta, Yasuhiro Takahashi

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 Å and 1.00 Å resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8% for 7.0-0.92 Å resolution data of the form I and 11.2% for the 13.3-1.0 Å resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 Å resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C α -C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D 2d symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.

Original languageEnglish
Pages (from-to)1155-1166
Number of pages12
JournalJournal of Molecular Biology
Volume315
Issue number5
DOIs
Publication statusPublished - Jan 1 2002
Externally publishedYes

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Ferredoxins
Bacillus
R388
Synchrotrons
Temperature
Clostridium
Hydrogen
Proteins
Radiation
Peptides
Direction compound

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms : Systematic distortion of [4Fe-4S] cluster in the protein. / Fukuyama, Keiichi; Okada, Toshihiro; Kakuta, Yoshimitsu; Takahashi, Yasuhiro.

In: Journal of Molecular Biology, Vol. 315, No. 5, 01.01.2002, p. 1155-1166.

Research output: Contribution to journalArticle

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abstract = "Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 {\AA} and 1.00 {\AA} resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8{\%} for 7.0-0.92 {\AA} resolution data of the form I and 11.2{\%} for the 13.3-1.0 {\AA} resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 {\AA} resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C α -C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D 2d symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.",
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