Alternative Model for Mechanism-Based Inhibition of Escherichia coli Ribonucleotide Reductase by 2′-Azido-2′-deoxyuridine 5′-Diphosphate

Ribonucleotide reductase (RDPR) from Escherichia coli is composed of two subunits, R1 and R2, and catalyzes the conversion of nucleotides to deoxynucleotides. The mechanism of inactivation of RDPR by 2′-azido-2′-deoxynucleoside 5′-diphosphate (N3UDP) has been examined using a variety of isotopically labeled derivatives: (1′-, 2′-, 3′-, or 4′-[²H])-N₃UDPs and 2′-[¹⁵N₃, ¹³C]-N₃UDP. Electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectroscopy studies using these compounds indicate that the 2′ carbon-nitrogen bond to the azide moiety is cleaved prior to or upon formation of the nitrogen-centered radical derived from the azide moiety of N₃UDP. EPR studies reveal no hyperfine interactions of the nitrogen-centered radical with the 1′, 2′, 3′, or 4′ hydrogens of N₃UDP. ESEEM studies however, reveal that the 1′ and 4′ deuterons are 3.3 ± 0.2 and 2.6 ± 0.3 Å, respectively, from the nitrogen-centered radical. Further support for carbon-nitrogen bond cleavage is derived from studies of the interaction of oxidized R1, C225SR1, and C462SR1 with R2 and N₃UDP. In all three cases, in contrast to the results with the wild type R1, azide is detected. Nitrogen-centered radical is not observed with either oxidized R1 or C225SR1 but is observed with C462SR1. These results suggest that C225 is required for the conversion of azide into N₂ and a nitrogen-centered radical. The dynamics of the inactivation of RDPR by N₃UDP have also been examined. Use of [3′-²H]N₃UDP reveals an isotope effect of ∼ 2 on the loss of the tyrosyl radical and the rate of inactivation of RDPR. In both cases the kinetics are complex, suggesting multiple modes of inactivation. In addition, several modes of inactivation are required to explain the observation that loss of the tyrosyl radical is slower than the rate of inactivation. Studies using [5′-³H]N₃UDP reveal that the rapid inactivation is the result of the formation of a tight noncovalent complex between modified nucleotide, nitrogen-centered radical and RDPR. Destruction of the nitrogen-centered radical is a slow process which appears to be accompanied by decomposition of the modified nucleotide into PPi, uracil, and 2-methylene-3(2H)-furanone. The latter covalently modifies R1 and ultimately leads to loss of ∼ 50% of the activity of R1.