Family 39 α-l-Iduronidases and β-d-Xylosidases React through Similar Glycosyl−Enzyme Intermediates: Identification of the Human Iduronidase Nucleophile

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Abstract
The inclusion of both β-d-xylosidases and α-l-iduronidases within the same sequence-related family (family 39), despite the considerable difference in substrate structures and poor sequence conservation around the putative nucleophile, raises concerns about whether a common mechanism is followed by the two enzymes. A novel anchimeric assistance mechanism for iduronidases involving a lactone intermediate is one possibility. NMR analysis of the methanolysis reaction catalyzed by human α-l-iduronidase reveals that, as with the β-d-xylosidases, α-l-iduronidase is a retaining glycosidase. Using two different mechanism-based inactivators, 5-fluoro-α-l-iduronyl fluoride and 2-deoxy-2-fluoro-α-l-iduronyl fluoride, the active site nucleophile in the human α-l-iduronidase was identified as Glu299 within the 295IYNDEAD301 sequence. The equivalent, though loosely predicted, glutamic acid was identified as the nucleophile in the family 39 β-d-xylosidase from Bacillus sp. [Vocadlo, D., et al. (1998) Biochem. J. 335, 449−455]; thus, a common mechanism involving a covalent glycosyl−enzyme intermediate that adopts the rather uncommon 2,5B conformation is predicted.