Structural and Kinetic Analysis of Carboxyl-Metabolizing Enzymes Understanding Active Site Architecture and Environmental Adaptation in Marine Carbon Cycling

Carboxyl-rich aliphatic compounds are represented as a significant fraction of marine dissolved organic matter, yet the enzymatic mechanisms governing their transformation remain poorly understood. A comprehensive analysis of four major enzyme families involved in carboxyl metabolism is presented in this study: decarboxylases, carboxylases, ring-cleaving dioxygenases, and omega-oxidation enzymes. Integrated structural analysis via FPocket and kinetic modeling were utilized to investigate how active site architecture influences catalytic efficiency across different marine environments. Distinct pocket geometries that correlate with substrate specificity and environmental adaptation strategies are revealed by the results. The highest sensitivity to pH and ionic strength variations is shown by decarboxylases (apparent Km changes of 2.3-fold), while remarkable adaptation to oxygen-limited deep-sea conditions is demonstrated by dioxygenases (Km of O2 reduced by 65%). Unique bi-substrate binding pockets optimized for CO2 fixation are exhibited by carboxylases, with Hill coefficients indicating positive cooperativity (n = 1.8 ± 0.3). Progressive substrate channeling mechanisms with 85% efficiency are displayed by omega-oxidation enzymes. New insights into marine carbon cycling mechanisms and enzyme evolution in aquatic environments are provided by these findings, with implications for understanding climate change impacts on oceanic biochemical processes.