9R5L

Crystal structure of class Ie ribonucleotide reductase R2 subunit from Mesoplasma florum with a D212N mutation

Summary for 9R5L

• Entry DOI: 10.2210/pdb9r5l/pdb
• Descriptor: ribonucleoside-diphosphate reductase (2 entities in total)
• Functional Keywords: ribonucleotide reductase r2e, class ie rnr, oxidoreductase, ferritin-like superfamily, nrdf, rnr beta-subunit
• Biological source: Mesoplasma florum L1
• Total number of polymer chains: 1
• Total formula weight: 39827.63

Authors

John, J.,Hogbom, M. (deposition date: 2025-05-09, release date: 2026-05-20)

Primary citation

Sirohiwal, A.,John, J.,Kutin, Y.,Kumar, R.,Baserga, F.,Srinivas, V.,Lebrette, H.,Poverlein, M.C.,Gamiz-Hernandez, A.P.,Heberle, J.,Kasanmascheff, M.,Hogbom, M.,Kaila, V.R.I.
Low-barrier hydrogen bond powers long-range radical transfer in the metal-free ribonucleotide reductase.
Proc.Natl.Acad.Sci.USA, 123:e2529856123-e2529856123, 2026

PubMed Abstract: Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotide (RNA) to deoxyribonucleotide (DNA) building blocks initiated by a long-range (>30 Å) proton-coupled electron transfer (PCET) by mechanistic principles that remain much debated. By combining multiscale quantum and classical simulations with directed mutagenesis, X-ray crystallography, and vibrational and electron paramagnetic resonance spectroscopy, we elucidate here the molecular principles underlying how metal-free RNRs initiate the long-range PCET process by creating a highly stable 3,4-dihydroxyphenylalanine (DOPA) initiator radical. We show that DOPA• is redox-tuned by a low-barrier hydrogen bond (LBHB), with a delocalized proton that provides the catalytic power for the ribonucleotide reduction. We find that the LBHB couples to an extended hydrogen-bonded network, with distant mutations resulting in the loss of radical formation, and providing key molecular insight into the long-range radical transport mechanism in RNRs. On a general level, our findings support the direct involvement of LBHB in protein chemistry and the importance of quantum effects in enzyme catalysis.

PubMed: 42096306
DOI: 10.1073/pnas.2529856123

Experimental method

X-RAY DIFFRACTION (1.7 Å)