A substrate radical intermediate in catalysis by the antibiotic resistance protein Cfr

The radical SAM enzyme Cfr catalyzes methylation of a ribosomal adenosine, causing broad antibiotic resistance. EPR and ENDOR techniques now provide direct evidence for the proposed enzymatic mechanism by detecting a central crosslinked intermediate in which a radical is located on the nucleotide. Cfr-dependent methylation of C8 of A2503 in 23S ribosomal RNA confers bacterial resistance to an array of clinically important antibiotics that target the large subunit of the ribosome, including the synthetic oxazolidinone antibiotic linezolid. The key element of the proposed mechanism for Cfr, a radical S-adenosylmethionine enzyme, is the addition of a methylene radical, generated by hydrogen-atom abstraction from the methyl group of an S-methylated cysteine, onto C8 of A2503 to form a protein–nucleic acid crosslinked species containing an unpaired electron. Herein we use continuous-wave and pulsed EPR techniques to provide direct spectroscopic evidence for this intermediate, showing a spin-delocalized radical with maximum spin density at N7 of the adenine ring. In addition, we use rapid freeze-quench EPR to show that the radical forms and decays with rate constants that are consistent with the rate of formation of the methylated product.