A geometric deep learning framework for genome-wide prediction of enzyme turnover number

Abstract Enzyme turnover numbers ( K cat ) are fundamental kinetic constants that quantify enzymatic efficiency. Systematic studies of K cat are essential for characterizing the mechanisms underlying proteomic composition and cellular metabolism. However, experimental measurements of K cat remain limited and prone to noise. To address this, we present KcatNet, a geometric deep learning model designed for high-throughput prediction of K cat in metabolic enzymes across all organisms, leveraging paired enzyme sequence and substrate representations. KcatNet consistently outperforms existing predictors, particularly for enzymes with high catalytic efficiency, and demonstrates strong generalization to enzymes that are dissimilar to those in the training set. Furthermore, KcatNet uncovers structural mechanisms and interaction patterns within enzyme-substrate complexes, providing insights into architectural principles that are inaccessible with existing methods by harnessing the representational power of large-scale protein language models. We applied KcatNet to genome-scale K cat prediction across diverse yeast species, improving proteome allocation predictions by integrating its outputs into metabolic models. Experimental validation further confirmed the model’s ability to identify enzyme mutants with enhanced activity. By bridging the gap between sequence, structure, and function, KcatNet establishes a robust foundation for advancing understanding of molecular-level mechanisms and accelerating enzyme engineering efforts.