Selenocysteine-dependent Enzymes: Structure, Function and Selenium-derived Mechanism

Selenocysteine (Sec), the 21st proteinogenic amino acid, is a structural analog of cysteine (Cys) where its sidechain sulfur atom is substituted by selenium. Sec typically serves as the catalytic site in Sec-dependent enzymes and therefore the distinct chemical properties of selenium compared to sulfur endow these enzymes with unique characteristics that differentiate them from their Cys-dependent counterparts. In this review, we provide a systematic and comparative analysis of well-characterized Sec-dependent enzymes alongside their naturally occurring and artificially engineered Cys-dependent analogs in the context of biological function, active-site structure, catalytic property and mechanistic insight. Our analysis reveals that Sec-dependent enzymes consistently exhibit higher catalytic activities than their Cys analogs, despite sharing common catalytic architectures and catalytic mechanisms. The kinetic advantage is primarily attributable to the stronger nucleophilicity and/or the enhanced leaving-group ability of the selenolate sidechain of Sec compared to that of Cys. Furthermore, the stronger electrophilicity of selenolate confers all reviewed redox enzymes with superior oxidative resistance, while the increased acidity of selenolate enables metal-dependent formate dehydrogenases and hydrogenases to favor their reductive reactions (i.e., CO₂ reduction and H₂ production, respectively). Interestingly, certain natural Cys-dependent thioredoxin reductases appear to have evolved compensatory mechanisms through active-site-residue modifications to mitigate catalytic inefficiencies arising from the absence of Sec. The summarized correspondence between the chemical properties of Sec and the catalytic advantages of Sec-dependent enzymes provides a mechanistic basis for optimizing their catalytic performance via engineering of the micro-environment of Sec.