Why can structural similarity coexist with different protein functions?

Why

Protein folds are often evolutionarily conserved because stable scaffolds support multiple chemistries. Small substitutions near an active site can alter substrate recognition, while insertions, domain organization, oligomerization or allosteric control can redirect function. Structural alignment alone does not establish orthology or the identity of a catalytic reaction.

Compare sequences, catalytic residues, pocket geometry, ligands, phylogeny and cellular localization, then test function with biochemical assays. For example, two enzymes may share a Rossmann-like nucleotide-binding fold yet catalyze distinct reactions using different catalytic groups. Predictions should express graded confidence and avoid transferring precise functional annotations solely from high global RMSD similarity.

When key residues are missing or the pocket is uncertain, favor broader superfamily-level annotation.