The Ntn-hydrolases (N-terminal nucleophile) are a
superfamily of diverse enzymes that has recently been
characterized. All of the proteins in this family are activated
autocatalytically; they contain an N-terminally located
catalytic nucleophile, and they cleave an amide bond. In
the present study, the structures of four enzymes of this
superfamily are compared in more detail. Although the amino
acid sequence homology is almost completely absent, the
enzymes share a similar αββα-core structure.
The central β-sheets in the core were found to have
different packing angles, ranging from 5 to 35°. In
the Ntn-hydrolases under study, eight totally conserved
secondary structure units were found (region C). Five of
them were observed to contain the greatest number of conserved
and functionally important residues and are therefore crucial
for the structure and function of Ntn-hydrolases. Two additional
regions, consisting of secondary structure units (regions
A and B), were found to be in structurally similar locations,
but in different orders in the polypeptide chain. The catalytic
machinery is located in the structures in a similar manner,
and thus the catalytic mechanisms of all of the enzymes
are probably similar. However, the substrate binding and
the oxyanion hole differed partially.