The Role of the Hydrogen Bond Network in Maintaining Heme Pocket Stability and Protein Function Specificity of <i>C. diphtheriae</i> Coproheme Decarboxylase

oleh: Federico Sebastiani, Chiara Baroni, Gaurav Patil, Andrea Dali, Maurizio Becucci, Stefan Hofbauer, Giulietta Smulevich

Format: Article
Diterbitkan: MDPI AG 2023-01-01

Deskripsi

Monoderm bacteria accumulate heme <i>b</i> via the coproporphyrin-dependent biosynthesis pathway. In the final step, in the presence of two molecules of H<sub>2</sub>O<sub>2</sub>, the propionate groups of coproheme at positions 2 and 4 are decarboxylated to form vinyl groups by coproheme decarboxylase (ChdC), in a stepwise process. Decarboxylation of propionate 2 produces an intermediate that rotates by 90° inside the protein pocket, bringing propionate 4 near the catalytic tyrosine, to allow the second decarboxylation step. The active site of ChdCs is stabilized by an extensive H-bond network involving water molecules, specific amino acid residues, and the propionate groups of the porphyrin. To evaluate the role of these H-bonds in the pocket stability and enzyme functionality, we characterized, via resonance Raman and electronic absorption spectroscopies, single and double mutants of the actinobacterial pathogen <i>Corynebacterium diphtheriae</i> ChdC complexed with coproheme and heme <i>b</i>. The selective elimination of the H-bond interactions between propionates 2, 4, 6, and 7 and the polar residues of the pocket allowed us to establish the role of each H-bond in the catalytic reaction and to follow the changes in the interactions from the substrate to the product.