8RZJ

ZgGH129 from Zobellia galactanivorans in complex with the inhibitor ADG-IF (3,6-anhydro-D-galacto-isofagomine).

This is a non-PDB format compatible entry.

Summary for 8RZJ

• Entry DOI: 10.2210/pdb8rzj/pdb
• Descriptor: Conserved hypothetical periplasmic protein, (1~{R},5~{R},8~{S})-6-oxa-3-azabicyclo[3.2.1]octan-8-ol, CHLORIDE ION, ... (9 entities in total)
• Functional Keywords: 3, 6-anhydro-d-galactosidase zobellia galactanivorans carrageenan oligosaccharide 3, 6-anhydro-d-galactose, hydrolase
• Biological source: Zobellia galactanivorans
• Total number of polymer chains: 4
• Total formula weight: 309354.27

Authors

Roret, T.,Czjzek, M.,Ficko-Blean, E. (deposition date: 2024-02-12, release date: 2024-07-31, Last modification date: 2024-10-23)

Primary citation

Wallace, M.D.,Cuxart, I.,Roret, T.,Guee, L.,Debowski, A.W.,Czjzek, M.,Rovira, C.,Stubbs, K.A.,Ficko-Blean, E.
Constrained Catalytic Itinerary of a Retaining 3,6-Anhydro-D-Galactosidase, a Key Enzyme in Red Algal Cell Wall Degradation.
Angew.Chem.Int.Ed.Engl., 63:e202411171-e202411171, 2024

PubMed 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.

PubMed: 39022920
DOI: 10.1002/anie.202411171

Experimental method

X-RAY DIFFRACTION (1.99 Å)