Constrained Catalytic Itinerary of a Retaining 3,6‐Anhydro‐D‐Galactosidase, a Key Enzyme in Red Algal Cell Wall Degradation

Abstract

The marine Bacteroidota Zobellia galactanivorans has a polysaccharide utilization locus dedicated to the catabolism of the red algal cell wall galactan carrageenan and its unique and industrially important α‐3,6‐anhydro‐D‐galactose (ADG) monosaccharide. Here we present the first analysis of the specific molecular interactions the exo‐(α‐1,3)‐3,6‐anhydro‐D‐galactosidase ZgGH129 uses to cope with the strict steric restrictions imposed by its bicyclic ADG substrate ‐ which is ring flipped relative to D‐galactose. Crystallographic snapshots of key catalytic states obtained with the natural substrate and novel chemical tools designed to mimic species along the reaction coordinate, together with quantum mechanics/molecular mechanics (QM/MM) metadynamics methods and kinetic studies, demonstrate a retaining mechanism where the second step is rate limiting. The conformational landscape of the constrained 3,6‐anhydro‐D‐galactopyranose ring proceeds through enzyme glycosylation B1,4 → [E4]‡ → E4/1C4 and deglycosylation E4/1C4 → [E4]‡ → B1,4 itineraries limited to the Southern Hemisphere of the Cremer‐Pople sphere. These results demonstrate the conformational changes throughout catalysis in a non‐standard, sterically restrained, bicyclic monosaccharide and provide a molecular framework for mechanism‐based inhibitor design for anhydro‐type carbohydrate‐processing enzymes and for future applications involving carrageenan degradation. In addition, it provides a rare example of distinct niche‐based conformational itineraries within the same carbohydrate‐active enzyme family.