alpha-1,4-Glucan lyase performs a trans-elimination via a nucleophilic displacement followed by a syn-elimination.

alpha-Glucan lyase (EC 4.2.2.13, GLase) cleaves alpha-1,4-glucosidic bonds via an elimination reaction to produce 1,5-d-anhydrofructose. GLase was inactivated by the mechanism based alpha-glucosidase inactivator, 5-fluoro-beta-l-idosyl fluoride. The trapped glycosyl-enzyme intermediate was isolated and the nucleophilic amino acid residue (Asp 553) identified is equivalent to the residue so identified in sequence-related alpha-glucosidases. This intermediate undergoes a syn-elimination reaction to release the product. Further evidence against a direct trans-elimination mechanism was provided by the absence of a primary kinetic isotope effect on the substrate substituted with deuterium at the C2 position.