8RZI

ZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,6-Anhydro-2-deoxy-2-fluoro-a-D-galactopyranosyl fluoride) resulting in a trapped glycosyl-enzyme intermediate.

これはPDB形式変換不可エントリーです。

8RZI の概要

• エントリーDOI: 10.2210/pdb8rzi/pdb
• 分子名称: Conserved hypothetical periplasmic protein, (1~{R},4~{S},5~{S},8~{S})-4-fluoranyl-2,6-dioxabicyclo[3.2.1]octan-8-ol, L(+)-TARTARIC ACID, ... (8 entities in total)
• 機能のキーワード: 3, 6-anhydro-d-galactosidase zobellia galactanivorans carrageenan oligosaccharide 3, 6-anhydro-d-galactose, hydrolase
• 由来する生物種: Zobellia galactanivorans
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 308120.70

構造登録者

Roret, T.,Czjzek, M.,Ficko-Blean, E. (登録日: 2024-02-12, 公開日: 2024-07-31, 最終更新日: 2024-10-23)

主引用文献

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 that 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 B→[E]→E/C and deglycosylation E/C→[E]→B 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, our study provides a rare example of distinct niche-based conformational itineraries within the same carbohydrate-active enzyme family.

PubMed: 39022920
DOI: 10.1002/anie.202411171

実験手法

X-RAY DIFFRACTION (1.96 Å)