Structure‐based sequence alignment for the β‐trefoil subdomain of the clostridial neurotoxin family provides residue level information about the putative ganglioside binding site

Clostridial neurotoxins embrace a family of extremely potent toxins comprised of tetanus toxin (TeNT) and seven different serotypes of botulinum toxin (BoNT/A–G). The β‐trefoil subdomain of the C‐terminal part of the heavy chain (HC), responsible for ganglioside binding, is the most divergent region in clostridial neurotoxins with sequence identity as low as 15%. We re‐examined the alignment between family sequences within this subdomain, since in this region all alignments published to date show obvious inconsistencies with the β‐trefoil fold. The final alignment was obtained by considering the general constraints imposed by this fold, and homology modeling studies based on the TeNT structure. Recently solved structures of BoNT/A confirm the validity of this structure‐based approach. Taking into account biochemical data and crystal structures of TeNT and BoNT/A, we also re‐examined the location of the putative ganglioside binding site and, using the new alignment, characterized this site in other BoNT serotypes.