Identification of the conserved spatial position of key active-site atoms in glycoside hydrolase 13 family members

A computational study on the glycoside hydrolase 13 (GH13) family of the CAZy database has been carried out at the atomic level in order to identify the conserved positions that may be responsible for recognition of the substrate. Analysis with substrate analog-, inhibitor-, or product-bound 3D structures was carried out to find the atomic spatial arrangement of the amino acids that make −2, −1, +1, and +2 subsites and water oxygen atoms around the ligand. The identified conserved positions of subsites were independent from the nature of the amino acid. The −1 and +1 subsites have more conserved positions than the −2 and +2 subsites. Some of the clusters of the −1 and +1 subsites have atoms of the same chemical nature. A spatially conserved position for water, which is stabilized by a hydrogen bond with the carboxyl group of a proton donor (Glu) and Asp of the catalytic triad, was found in the −1 subsite of 75% of the enzymes subjected to analysis. This position could be the region of hydrolytic water.