Catalytic activity of a ζ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms

Abstract

The carbonic anhydrase is the enzyme that catalyzes the reversible hydration of carbon dioxide and represents one of the most ancient proteins to which a plethora of works was devoted. The three main classes rely on zinc ion for activity. Most recently a new class of CA was discovered in marine diatoms to use naturally a cadmium ion as catalytic metal. In the present investigation we focused our attention on a carbonic anhydrase cambialistic enzyme (CDCA1) belonging to this new class. The study was inspired by the discovery that the replacement of zinc ion with cadmium does not entail significant differences in the catalytic performance of the enzyme. Our aim was to give further insight of the enzymatic work mechanism. Different possible reaction paths were considered for both metallic forms of the enzyme and comparison with previous studies concerning other carbonic anhydrases was made. The effects of the solvent on the energetics of the catalytic process, was also taken into account by means of a polarizable continuum model. The results obtained from density functional calculations, using a well consolidated mixing of exchange–correlation potential and basis set, and performed with a model of the active site designed on the basis of the X-ray crystal structure, proposed for both metal ions similar reaction pathways consisting in the nucleophilic attack by the metal bound hydroxide to the carbon dioxide with bicarbonate formation, in a next internal rotation of this last fragment, and then in the formation of a species ready for the product removal. Similar activation barriers were found in the rate determining steps that confirm the experimental indication concerning the comparable efficiency of the enzyme in the presence of a zinc or cadmium metal ion.