Human lysosomal and jack bean alpha-mannosidases are retaining glycosidases.
Identification of Asp197 as the catalytic nucleophile in the family 38 alpha-mannosidase from bovine kidney lysosomes.
X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 52-999.
The structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation.
Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase.
This enzyme belongs to glycosyl hydrolase family-38. Although the nucleophilic residue, Asp125 (of 2wyh), is bound to zinc ion in the apo enzyme, it does not seem to be bound to the zinc ion while the substrate/product is bound to the active site on this enzyme. During the reaction, the zinc ion is bound to the hydroxyl groups of the mannoside, as well as to His13 and Asp15. Thus, the reaction of this enzyme proceeds as follows (see [3] & [4]): (0) Arg149 and Tyr192 modulate the activity of the nucleophilic residue, Asp125, by interacting with it. (1) Asp232 acts as a general acid to protonate the oxygen atom of the leaving group, leading to the formation of oxocarbenium-ion like transition-state (in a 1S5 skew-boat conformation). Here, the skew-boat conformation of the transition-state seems to be stabilized by the zinc ion, which is bound to His13 and Asp15. (2) Asp125 makes a nucleophilic attack on the C1 atom of the alpha-mannoside in the oxocarbenium-ion like transition-state, forming a covalent glycosyl-enzyme intermediate. (This nucleophilic substitution seems to be SN1-like raction.) (3) Asp232 now acts as a general base to activate a water molecule. The activated water makes a nucleophilic attack on the glycosyl-enzyme intermediate, leading to the formation of oxocarbenium-ion like transition-state. The transition-state is also stabilized by the zinc ion. (4) Finally, the bond between the alpha-mannose and Asp125 is cleaved, while the bond between the alpha-mannose and the activated water is formed, to complete the reaction.