Computational Prediction of Metal Binding Sites in Lysyl aminopeptidase in Pyrococcus furiosus (strain ATCC 43587)

More than 70,000 protein structures are currently found in the Protein Data Bank, and approximately one-third contain metal ions essential for function. Identifying and characterizing metal ion–binding sites experimentally is time-consuming and costly. Recently, the three-dimensional structure of two aminopeptidases, the methionine aminopeptidase from Escherichia coli and the leucine aminopeptidase from Aeromonas proteolytica, have been elucidated by crystallographic studies. Aminopeptidases play a role in several important physiological processes. It is noteworthy that some of them take part in the catabolism of exogenously supplied peptides and are necessary for the final steps of protein turnover. The object of the present study is to characterize the metal binding sites of lysine aminopeptidase (KAP) from the hyperthermophilic archaeon, P. furiosus. It is shown that the P. furiosus enzyme, while having the same narrow substrate specificity as the KAPs from S. cerevisiae and A. niger, contains conserved sequences that are homologous to those of members of the M18 rather than M1 family of peptidases. In contrast to the large M1 family, only two members of the M18 family have been characterized. These are a leucyl aminopeptidase from yeast and an aspartyl aminopeptidase from rabbit. Herein, we therefore report characterization of the first KAP from an archaeon, in the form of the P. furiosus enzyme, which is also the first prokaryotic member of the M18 family.