Greenase: A Comprehensive Database for Carbon-fixing Enzyme Retrieval

ABSTRACT Carbon fixation plays a critical role in mitigating climate change and enabling sustainable biomanufacturing. Here, we presented Greenase, an integrated database and analysis platform for carbon-fixing enzymes, that combined high-quality enzyme information, structural clustering, and an auxiliary enzyme recommendation module. In contrast to existing databases, Greenase integrates structural clustering and enzyme recommendation module. The structural clustering reveals the internal structural diversity of enzyme families, while the auxiliary module for enzyme recommendation based on molecular similarity can help identify enzymes that potentially catalyze structurally similar substrates to support novel enzyme discovery and metabolic pathway design. Case studies on the formolase pathway and Rubisco expression demonstrate the practical advantages of this platform in enzyme selection, pathway optimization, and experimental validation. Greenase provides a robust and expandable resource for carbon fixation and conversion research that supports novel enzyme discovery, metabolic pathway optimization, and enzyme engineering while guiding future data expansion and functional validation.