8rzk

The Michaelis complex of ZgGH129 D486N from Zobellia galactanivorans with neo-b/k-oligo-carrageenan tetrasaccharide (beta-kappa neo-oligo-carrageenan DP4).

spinqualitylabelsall models 8rzk, resolution 2.29Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8rzk is a 4 chain structure with sequence from Zobellia galactanivorans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.29Å Ligands: 9RN, CL, EDO, G4S, GAL, NA, TLA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function G0L004_ZOBGA Publication Abstract from PubMed 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 alpha-3,6-anhydro-D-galactose (ADG) monosaccharide. Here we present the first analysis of the specific molecular interactions the exo-(alpha-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]double dagger --> E4/1C4 and deglycosylation E4/1C4 --> [E4]double dagger --> 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. Constrained Catalytic Itinerary of a Retaining 3,6-Anhydro-D-Galactosidase, a Key Enzyme in Red Algal Cell Wall Degradation.,Wallace MD, Cuxart I, Roret T, Guee L, Debowski AW, Czjzek M, Rovira C, Stubbs KA, Ficko-Blean E Angew Chem Int Ed Engl. 2024 Jul 18:e202411171. doi: 10.1002/anie.202411171. PMID:39022920 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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