Structural comparison of Ntn-hydrolases

The Ntn-hydrolases (N-terminal nucleophile) are a superfamily of diverse en zymes that has recently been characterized. All of the proteins in this fam ily are activated autocatalytically; they contain an N-terminally located c atalytic nucleophile, and they cleave an amide bond. In the present study, the structures of four enzymes of this superfamily are compared in more det ail. Although the amino acid sequence homology is almost completely absent, the enzymes share a similar alpha beta beta alpha -core structure. The cen tral beta -sheets in the core were found to have different packing angles, ranging from 5 to 35 degrees. In the Ntn-hydrolases under study, eight tota lly 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 functio n of Ntn-hydrolases. Two additional regions, consisting of secondary struct ure units (regions A and B), were found to be in structurally similar locat ions, but in different orders in the polypeptide chain. The catalytic machi nery is located in the structures in a similar manner, and thus the catalyt ic mechanisms of all of the enzymes are probably similar. However, the subs trate binding and the oxyanion hole differed partially.