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Instruments / Technical Area	Publication Details	Published	Actions
I04-Macromolecular Crystallography	Characterization of a second class Ie ribonucleotide reductase Juliane John , Daniel Lundin , Rui M. Branca , Rohit Kumar , Vivek Srinivas , Hugo Lebrette , Martin Högbom Communications Biology 8 DOI: 10.1038/s42003-025-07565-3 Diamond Proposal Number(s): [29948] Open Access Show Abstract ▼ Abstract: Class I ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides under oxic conditions. The R2 subunit provides a radical required for catalysis conducted by the R1 subunit. In most R2s the radical is generated on a tyrosine via oxidation by an adjacent metal site. The discovery of a metal-free R2 defined the new RNR subclass Ie. In R2e, three of the otherwise strictly conserved metal-binding glutamates in the active site are substituted. Two variants have been found, VPK and QSK. To date, the VPK version has been the focus of biochemical characterization. Here we characterize a QSK variant of R2e. We analyse the organismal distribution of the two R2e versions and find dozens of organisms relying solely on the QSK RNR for deoxyribonucleotide production. We demonstrate that the R2eQSK of the human pathogen Gardnerella vaginalis (Bifidobacterium vaginale) modifies the active site-adjacent tyrosine to DOPA. The amount of modified protein is shown to be dependent on coexpression with the other proteins encoded in the RNR operon. The DOPA containing R2eQSK can support ribonucleotide reduction in vitro while the unmodified protein cannot. Finally, we determined the first structures of R2eQSK in the unmodified and DOPA states.	Feb 2025
	Structure of a ribonucleotide reductase R2 protein radical Hugo Lebrette , Vivek Srinivas , Juliane John , Oskar Aurelius , Rohit Kumar , Daniel Lundin , Aaron S. Brewster , Asmit Bhowmick , Abhishek Sirohiwal , In-Sik Kim , Sheraz Gul , Cindy Pham , Kyle D. Sutherlin , Philipp Simon , Agata Butryn , Pierre Aller , Allen M. Orville , Franklin D. Fuller , Roberto Alonso-Mori , Alexander Batyuk , Nicholas K. Sauter , Vittal K. Yachandra , Junko Yano , Ville R. I. Kaila , Britt-Marie Sjöberg , Jan Kern , Katarina Roos , Martin Högbom Science 382, 109 - 113 DOI: 10.1126/science.adh8160 Show Abstract ▼ Abstract: Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.	Oct 2023

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