7Z3D

XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus

Summary for 7Z3D

• Entry DOI: 10.2210/pdb7z3d/pdb
• Descriptor: Ribonucleoside-diphosphate reductase subunit beta, Protein NrdI, MANGANESE (II) ION, ... (6 entities in total)
• Functional Keywords: ribonucleotide reductase r2b, class ib rnr, flavoprotein, metalloenzyme, oxidoreductase, ferritin-like superfamily, dimanganese cofactor, xfel
• Biological source: Bacillus cereus ATCC 14579; More
• Total number of polymer chains: 2
• Total formula weight: 51176.48

Authors

John, J.,Lebrette, H.,Aurelius, O.,Hogbom, M. (deposition date: 2022-03-02, release date: 2022-09-21, Last modification date: 2024-01-31)

Primary citation

John, J.,Aurelius, O.,Srinivas, V.,Saura, P.,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.,Kaila, V.R.I.,Kern, J.,Lebrette, H.,Hogbom, M.
Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography.
Elife, 11:-, 2022

PubMed 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 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 interaction 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.

PubMed: 36083619
DOI: 10.7554/eLife.79226

Experimental method

X-RAY DIFFRACTION (2 Å)