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Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography

John, Juliane ; Aurelius, Oskar LU ; Srinivas, Vivek ; Saura, Patricia ; Kim, In Sik ; Bhowmick, Asmit ; Simon, Philipp S. ; Dasgupta, Medhanjali ; Pham, Cindy and Gul, Sheraz , et al. (2022) In eLife 11.
Abstract

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation.... (More)

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced super-oxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
eLife
volume
11
article number
e79226
publisher
eLife Sciences Publications
external identifiers
  • pmid:36083619
  • scopus:85138126660
ISSN
2050-084X
DOI
10.7554/ELIFE.79226
language
English
LU publication?
yes
id
cbe346c3-34fa-43dd-aaad-cf57cfc37fd7
date added to LUP
2022-12-01 14:52:44
date last changed
2024-04-18 04:44:17
@article{cbe346c3-34fa-43dd-aaad-cf57cfc37fd7,
  abstract     = {{<p>Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O<sub>2</sub> interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced super-oxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.</p>}},
  author       = {{John, Juliane and Aurelius, Oskar and Srinivas, Vivek and Saura, Patricia and Kim, In Sik and Bhowmick, Asmit and Simon, Philipp S. and Dasgupta, Medhanjali and Pham, Cindy and Gul, Sheraz and Sutherlin, Kyle D. and Aller, Pierre and Butryn, Agata and Orville, Allen M. and Cheah, Mun Hon and Owada, Shigeki and Tono, Kensuke and Fuller, Franklin D. and Batyuk, Alexander and Brewster, Aaron S. and Sauter, Nicholas K. and Yachandra, Vittal K. and Yano, Junko and Kaila, Ville R.I. and Kern, Jan and Lebrette, Hugo and Högbom, Martin}},
  issn         = {{2050-084X}},
  language     = {{eng}},
  publisher    = {{eLife Sciences Publications}},
  series       = {{eLife}},
  title        = {{Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography}},
  url          = {{http://dx.doi.org/10.7554/ELIFE.79226}},
  doi          = {{10.7554/ELIFE.79226}},
  volume       = {{11}},
  year         = {{2022}},
}