Structural analysis of the Mn(IV)/Fe(III) cofactor of Chlamydia trachomatis ribonucleotide reductase by extended X-ray absorption fine structure spectroscopy and density functional theory calculations

The class Ic ribonucleotide reductase from Chlamydia trachomatis (Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of ∼2.92 Å. The Mn data also suggest the presence of a short 1.74 Å Mn-O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe₂(III/III) form of the protein. Models are differentiated by the protonation states of their bridging and terminal OH_x ligands as well as the location of the Mn(IV) ion (site 1 or 2). The models that agree best with experimental observation feature a μ-1,3-carboxylate bridge (E120), terminal solvent (H₂O/OH) to site 1, one μ-O bridge, and one μ-OH bridge. The site-placement of the metal ions cannot be discerned from the available data.