Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation

Abstract

Coproheme decarboxylases (ChdCs) catalyze the final step in heme <i>b</i> biosynthesis of monoderm and some diderm bacteria. In this reaction, coproheme is converted to heme <i>b</i> via monovinyl monopropionate deuteroheme (MMD) in two consecutive decarboxylation steps. In Firmicutes decarboxylation of propionates 2 and 4 of coproheme depend on hydrogen peroxide and the presence of a catalytic tyrosine. Here we demonstrate that ChdCs from Actinobacteria are unique in using a histidine (H118 in ChdC from <i>Corynebacterium diphtheriae</i>, <i>Cd</i>ChdC) as a distal base in addition to the redox-active tyrosine (Y135). We present the X-ray crystal structures of coproheme-<i>Cd</i>ChdC and MMD-<i>Cd</i>ChdC, which clearly show (i) differences in the active site architecture between Firmicutes and Actinobacteria and (ii) rotation of the redox-active reaction intermediate (MMD) after formation of the vinyl group at position 2. Distal H118 is shown to catalyze the heterolytic cleavage of hydrogen peroxide (<i>k</i> _app = (4.90 ± 1.25) × 10⁴ M^-1 s^-1). The resulting Compound I is rapidly converted to a catalytically active Compound I* (oxoiron(IV) Y135^•) that initiates the radical decarboxylation reactions. As a consequence of the more efficient Compound I formation, actinobacterial ChdCs exhibit a higher catalytic efficiency in comparison to representatives from Firmicutes. On the basis of the kinetic data of wild-type <i>Cd</i>ChdC and the variants H118A, Y135A, and H118A/Y135A together with high-resolution crystal structures and molecular dynamics simulations, we present a molecular mechanism for the hydrogen peroxide dependent conversion of coproheme via MMD to heme <i>b</i> and discuss differences between ChdCs from Actinobacteria and Firmicutes.