8BT3

Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, catalytically active radical state solved by XFEL

Summary for 8BT3

• Entry DOI: 10.2210/pdb8bt3/pdb
• Descriptor: Ribonucleoside-diphosphate reductase beta chain (2 entities in total)
• Functional Keywords: ribonucleotide reductase r2 subunit, ferritin-like superfamily, dopa post-translational modification, oxidoreductase
• Biological source: Mesoplasma florum L1
• Total number of polymer chains: 1
• Total formula weight: 39844.61

Authors

Lebrette, H.,Srinivas, V.,Hogbom, M. (deposition date: 2022-11-27, release date: 2023-11-01, Last modification date: 2024-11-13)

Primary citation

Lebrette, H.,Srinivas, V.,John, J.,Aurelius, O.,Kumar, R.,Lundin, D.,Brewster, A.S.,Bhowmick, A.,Sirohiwal, A.,Kim, I.S.,Gul, S.,Pham, C.,Sutherlin, K.D.,Simon, P.,Butryn, A.,Aller, P.,Orville, A.M.,Fuller, F.D.,Alonso-Mori, R.,Batyuk, A.,Sauter, N.K.,Yachandra, V.K.,Yano, J.,Kaila, V.R.I.,Sjoberg, B.M.,Kern, J.,Roos, K.,Hogbom, M.
Structure of a ribonucleotide reductase R2 protein radical.
Science, 382:109-113, 2023

PubMed 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.

PubMed: 37797025
DOI: 10.1126/science.adh8160

Experimental method

X-RAY DIFFRACTION (1.5 Å)