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

John, J.; Aurelius, O.; Srinivas, V.; Kim, I.-S.; Bhowmick, A.; Simon, P. S.; Dasgupta, M.; Pham, C.; Gul, S.; Sutherlin, K. D.; Aller, P.; Butryn, A.; Orville, A. M.; Cheah, M. H.; Owada, S.; Tono, K.; Fuller, F. D.; Batyuk, A.; Brewster, A. S.; Sauter, N. K.; Yachandra, V. K.; Yano, J.; Kern, J.; Lebrette, H.; Hogbom, M.

doi:10.1101/2022.04.14.488295

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bioRxiv · 10.1101/2022.04.14.488295

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

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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. We show that the flavin in the hydroquinone state is under steric strain in the R2b-NrdI protein complex, presumably tuning its redox potential to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2-interacton site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide 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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John, J., Aurelius, O., Srinivas, V., Kim, I.-S., Bhowmick, A., Simon, P. S., Dasgupta, M., Pham, C., Gul, S., Sutherlin, K. D., Aller, P., Butryn, A., Orville, A. M., Cheah, M. H., Owada, S., Tono, K., Fuller, F. D., Batyuk, A., Brewster, A. S., Sauter, N. K., Yachandra, V. K., Yano, J., Kern, J., Lebrette, H., Hogbom, M.. 2022-04-14. Redox-controlled structural reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography. https://doi.org/10.1101/2022.04.14.488295

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