Generation of the R2 Subunit of Ribonucleotide Reductase by Intein Chemistry: Insertion of 3-Nitrotyrosine at Residue 356 as a Probe of the Radical Initiation Process

Escherichia coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates. The enzyme is composed of two subunits: R1 and R2. R1 contains the active site for nucleotide reduction and the allosteric effector sites that regulate the specificity and turnover rate. R2 contains the diferric-tyrosyl (Y^.) radical cofactor that initiates nucleotide reduction by a putative long-range proton-coupled electron transfer (PCET) pathway over 35 Å. This pathway is thought to involve specific amino acid radical intermediates (Y122 to W48 to Y356 within R2 to Y731 to Y730 to C439 within R1). In an effort to study radical initiation, R2 (375 residues) has been synthesized semisynthetically. R2 (residues 1-353), attached to an intein and a chitin binding domain, was constructed, and the protein was expressed (construct 1). This construct was then incubated with Fe²⁺ and O₂ to generate the diferric-Y^. cofactor, and the resulting protein was purified using a chitin affinity column. Incubation of construct 1 with 2-mercaptoethanesulfonic acid (MESNA) resulted in the MESNA thioester of R2 (1-353) (construct 2). A peptide containing residues 354-375 of R2 was generated using solid-phase peptide synthesis where 354, a serine in the wild-type (wt) R2, was replaced by a cysteine. Construct 2 and this peptide were ligated, and the resulting full-length R2 was separated from truncated R2 by anion-exchange chromatography. The purified protein had a specific activity of 350 nmol min^-1 mg^-1, identical to the same protein generated by site-directed mutagenesis when normalized for Y^.. As a first step in studying the radical initiation by PCET, R2 was synthesized with Y356 replaced by 3-nitrotyrosine (NO₂Y). The protein is inactive (specific activity 1 × 10^-4 that of wt-R2), which permitted a determination of the pK_a of the NO₂Y in the R1/R2 complex in the presence of substrate and effectors. Under all conditions, the pK_a was minimally perturbed. This has important mechanistic implications for the radical initiation process.