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Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access

Grāve, Kristīne ; Lambert, Wietske LU ; Berggren, Gustav ; Griese, Julia J. ; Bennett, Matthew D. LU ; Logan, Derek T. LU and Högbom, Martin (2019) In Journal of Biological Inorganic Chemistry 24(6). p.849-861
Abstract

Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y·) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 Å) and in complex with manganese (MnII/MnII, 1.30 Å). We also report three structures of the protein in complex with iron, either prepared anaerobically (FeII/FeII form, 1.32 Å), or prepared aerobically in the photo-reduced FeII/FeII form (1.63 Å) and with the partially... (More)

Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y·) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 Å) and in complex with manganese (MnII/MnII, 1.30 Å). We also report three structures of the protein in complex with iron, either prepared anaerobically (FeII/FeII form, 1.32 Å), or prepared aerobically in the photo-reduced FeII/FeII form (1.63 Å) and with the partially oxidized metallo-cofactor (1.46 Å). The structures reveal significant conformational dynamics, likely to be associated with the generation, stabilization, and transfer of the radical to the R1 subunit. Based on observed redox-dependent structural changes, we propose that the passage for the superoxide, linking the FMN cofactor of NrdI and the metal site in NrdF, is closed upon metal oxidation, blocking access to the metal and radical sites. In addition, we describe the structural mechanics likely to be involved in this process.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Carboxylate shift, Ferritin superfamily, Metalloprotein, Oxidoreductase, X-ray crystallography
in
Journal of Biological Inorganic Chemistry
volume
24
issue
6
pages
849 - 861
publisher
Springer
external identifiers
  • scopus:85070873182
ISSN
0949-8257
DOI
10.1007/s00775-019-01703-z
language
English
LU publication?
yes
id
039a0ba9-c0be-40fe-bbaf-b5647968f12b
date added to LUP
2019-09-09 11:15:22
date last changed
2020-01-22 07:46:01
@article{039a0ba9-c0be-40fe-bbaf-b5647968f12b,
  abstract     = {<p>Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y·) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 Å) and in complex with manganese (Mn<sup>II</sup>/Mn<sup>II</sup>, 1.30 Å). We also report three structures of the protein in complex with iron, either prepared anaerobically (Fe<sup>II</sup>/Fe<sup>II</sup> form, 1.32 Å), or prepared aerobically in the photo-reduced Fe<sup>II</sup>/Fe<sup>II</sup> form (1.63 Å) and with the partially oxidized metallo-cofactor (1.46 Å). The structures reveal significant conformational dynamics, likely to be associated with the generation, stabilization, and transfer of the radical to the R1 subunit. Based on observed redox-dependent structural changes, we propose that the passage for the superoxide, linking the FMN cofactor of NrdI and the metal site in NrdF, is closed upon metal oxidation, blocking access to the metal and radical sites. In addition, we describe the structural mechanics likely to be involved in this process.</p>},
  author       = {Grāve, Kristīne and Lambert, Wietske and Berggren, Gustav and Griese, Julia J. and Bennett, Matthew D. and Logan, Derek T. and Högbom, Martin},
  issn         = {0949-8257},
  language     = {eng},
  number       = {6},
  pages        = {849--861},
  publisher    = {Springer},
  series       = {Journal of Biological Inorganic Chemistry},
  title        = {Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access},
  url          = {http://dx.doi.org/10.1007/s00775-019-01703-z},
  doi          = {10.1007/s00775-019-01703-z},
  volume       = {24},
  year         = {2019},
}