Recognition of active and inactive catalytic triads: A template based approach

It is well established that a sequence template along with the database is a powerful tool for identifying the biological function of proteins. Here, we describe a method for predicting the catalytic nature of certain proteins among the several protein structures deposited in the Protein Data Bank (PDB). For the present study, we considered a catalytic triad template (Ser-His-Asp) found in serine proteases. We found that a geometrically optimized active site template can be used as a highly selective tool for differentiating an active protein among several inactive proteins, based on their Ser-His-Asp interactions. For any protein to be proteolytic in nature, the bond angle between Ser Oγ–Ser Hγ⋯His Nɛ2 in the catalytic triad needs to be between 115° and 140°. The hydrogen bond distance between Ser Hγ⋯His Nɛ2 is more flexible in nature and it varies from 2.0 Å to 2.7 Å while in the case of His Hδ1⋯Asp Oδ1, it is from 1.6 Å to 2.0 Å. In terms of solvent accessibility, most of the active proteins lie in the range of 10–16 Å2, which enables easy accessibility to the substrate. These observations hold good for most catalytic triads and they can be employed to predict proteolytic nature of these catalytic triads.