Structure of the Nitrogen-Centered Radical Formed during Inactivation of E. coli Ribonucleotide Reductase by 2‘-Azido-2‘-deoxyuridine-5‘-diphosphate:  Trapping of the 3‘-Ketonucleotide

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides providing the monomeric precursors required for DNA replication and repair. The class I RNRs are composed of two homodimeric subunits:  R1 and R2. R1 has the active site where nucleotide reduction occurs, and R2 contains the diiron tyrosyl radical (Y•) cofactor essential for radical initiation on R1. Mechanism-based inhibitors, such as 2‘-azido-2‘-deoxyuridine-5‘-diphosphate (N₃UDP), have provided much insight into the reduction mechanism. N₃UDP is a stoichiometric inactivator that, upon interaction with RNR, results in loss of the Y• in R2 and formation of a nitrogen-centered radical (N•) covalently attached to C225 (R−S−N•−X) in the active site of R1. N₂ is lost prior to N• formation, and after its formation, stoichiometric amounts of 2-methylene-3-furanone, pyrophosphate, and uracil are also generated. On the basis of the hyperfine interactions associated with N•, it was proposed that N• is also covalently attached to the nucleotide through either the oxygen of the 3‘-OH (R−S−N•−O−R‘) or the 3‘-C (R−S−N•−C−OH). To distinguish between the proposed structures, the inactivation was carried out with 3‘-[¹⁷O]-N₃UDP and N• was examined by 9 and 140 GHz EPR spectroscopy. Broadening of the N• signal was detected and the spectrum simulated to obtain the [¹⁷O] hyperfine tensor. DFT calculations were employed to determine which structures are in best agreement with the simulated hyperfine tensor and our previous ESEEM data. The results are most consistent with the R−S−N•−C−OH structure and provide evidence for the trapping of a 3‘-ketonucleotide in the reduction process.