Conformational exceptions in glycoside hydrolase reactivity

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ID: 329670
2026
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Abstract
Abstract Glycoside hydrolases (GHs) accelerate glycosidic bond cleavage by coupling active-site architecture, the geometry required for substitution at the anomeric center, and the conformational landscape of the −1 sugar. This coupling is often summarized as family-dependent conformational itineraries that connect Michaelis complexes to oxocarbenium-ion-like transition states (and, for retaining enzymes, to covalent intermediates). However, crystallographic snapshots sometimes reveal complexes in which the −1 sugar remains close to a ground-state-like 4C₁ chair or adopts noncanonical puckers such as E₅. In this Review, we reassess such observations within a cautious physical-organic framework. Here, “exception” is used in a mechanistic rather than statistical sense: the aim is to document and interpret departures from the conformational behaviour expected from accepted stereochemistry itinerary relationships, not to estimate the relative abundance of such cases in the Protein Data Bank. Chair-like 4C₁ complexes should not be interpreted as evidence for a new transition-state geometry; rather, they may represent recognition or pre-reactive minima in which catalytic residues are positioned near C1 but additional late, transient, or ensemble distortion is still required to reach an in-line, oxocarbenium-ion-like transition state. We further discuss how metal coordination and active-site constraints in α-mannosidases can stabilize alternative pre-reactive basins—exemplified by E₅ complexes in GH38 and GH92—while preserving access to transition-state-competent regions. Finally, we outline how structural descriptors, on-enzyme dynamics, and intrinsic quantum-mechanical “preactivation” indices can help distinguish genuinely productive noncanonical states from crystallographic ground-state snapshots.
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Authors Santiago Alonso‐Gil
Journal glycobiology
Year 2026
DOI
10.1093/glycob/cwag082
URL
https://doi.org/10.1093/glycob/cwag082
Keywords Keywords not found

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