Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase

Conformational dynamics is important for enzyme catalysis. However, engineering dynamics to achieve a higher catalytic efficiency is still challenging. In this work, we develop a new strategy to improve the activity of yeast cytosine deaminase (yCD) by engineering its conformational dynamics. Specifically, we increase the dynamics of the yCD C-terminal helix, an active site lid that controls the product release. The C-terminal is extended by a dynamical single a-helix (SAH), which improves the product release rate by up to similar to 8-fold, and the overall catalytic rate k(cat) by up to similar to 2-fold. It is also shown that the k(cat) increase is due to the favorable activation entropy change. The NMR H/D exchange data indicate that the conformational dynamics of the transition state analog complex increases as the helix is extended, elucidating the origin of the enhanced catalytic entropy. This study highlights a novel dynamics engineering strategy that can accelerate the overall catalysis through the entropy-driven mechanism.

Automated summary

Conformational dynamics plays a crucial role in enzyme catalysis, and engineering these dynamics to improve catalytic efficiency remains challenging. In this study, a new strategy is developed to enhance the activity of yeast cytosine deaminase by modulating its conformational dynamics. By extending the C-terminal helix, which serves as an active site lid, the product release rate and overall catalytic rate are significantly increased. The favorable activation entropy change is identified as the main contributor to the improved catalytic efficiency. This study introduces a novel dynamics engineering approach that accelerates catalysis through an entropy-driven mechanism.