Relationship between active site structure and chemistry in dioxygen producing chlorite dismutases

This thesis focuses on understanding the relationship between the active site structure and function in the heme-containing enzyme chlorite dismutase from Dechloromonas aromatica (DaCld). DaCld decomposes chlorite (ClO2-) into chloride (Cl-) and oxygen (O2) via an efficient reaction that is nearly diffusion controlled.

Due to the existence of advanced structure-activity models for heme peroxidases and the similarity of the behavior of peroxide and chlorite as substrates, we initiated our structure-function studies in 2008 by analogy to these enzymes. In 2009, the crystal structures of DaCld and a second Cld were solved for the first time, allowing us to consider the influence of structural elements directly. We investigated the role of an arginine residue (Arg183) in the pocket above the heme plane in catalysis using diverse biochemistry, molecular biology and spectroscopy techniques (notably stopped-flow, resonance Raman, UV/Visible). We mutated this residue, which has an alkylguanidinium side chain, to lysine (primary amine), glutamine (alkylamide), and alanine (methyl), and studied both the native (wild type, WT) and modified forms. We had found earlier that the rate of catalysis and several spectroscopic properties of the WT protein are pH-dependent. We proposed that this was either due to acid/base chemistry at Arg183 (analogous to an active-site His in peroxidase), or to the mobility of its side chain due to pH-dependent hydrogen bond formation/cleavage. The latter model was most consistent with the available data; particularly resonance Raman (rR) data for the ferrous carbonyl form of WT and mutant proteins. By reacting the protein with peracids, we were able to characterize Compound I (oxoferryl porphyrin radical) which decays to a Compound ES-like species where the porphyrin radical migrates to a nearby tryptophan residue. We mutated three conserved tryptophan residues in DaCld's active site in order to attempt to block off radical migration and stabilize Compound I.

The ability of DaCld to produce such a great amount of oxygen can be used for other needs, for example in the prevention of tissue necrosis. DaCld offers the possibility of production of O2 in situ in a regulated fashion and without generation of toxic byproducts.