Updating the sequence based classification of glycosyl hydrolases
Additionally, certain enzymes can catalyze reactions that fall in more than one class. Two reaction mechanisms are most commonly found for the retaining and inverting enzymes, as first outlined by Koshland and as described below. However several interesting variations on these mechanisms have been found, and one fundamentally different mechanism, catalyzed by an NADH cofactor, has been discovered in recent years, as discussed below.
Sequence-based classification uses algorithmic methods to assign sequences to various families.
If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number.
A necessary consequence of the EC classification scheme is that codes can be applied only to enzymes for which a function has been biochemically identified.
All information on these pages should therefore be considered to be under revision and may be subject to major changes.Since the seminal sequence-based classification of GHs into families, it has subsequently been observed that some of these families also group non-hydrolytic enzymes and proteins, due to sequence and structural similarity [1, 2, 3, 4, 5, 6, 7, 8].In many cases, these alternative activities bear some degree of mechanistic similarity (e.g., conserved catalytic residues or enzyme intermediates) to the eponymous enzymes: These pages have been approved by the Responsible Curator as essentially complete.One notable exception is the glycoside hydrolases of family GH97, which contains both retaining and inverting enzymes; a glutamate acts as a general base in inverting members, whereas an aspartate likely acts as a catalytic nucleophile in retaining members .Another mechanistic curiosity are the glycoside hydrolases of familes GH4 and GH109 which operate through an NAD-dependent hydrolysis mechanism that proceeds through oxidation-elimination-addition-reduction steps via anionic transition states .