The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease

Background: The N-terminal pyroglutamyl (pGlu) residue of peptide hormones, such as thyrotropin-releasing hormone (TRH) and luteinizing hormone releas ing hormone (LH-RH), confers resistance to proteolysis by conventional amin opeptidases. Specialized pyroglutamyl peptidases (PGPs) are able to cleave an N-terminal pyroglutamyl residue and thus control hormonal signals. Until now, no direct or homology-based three-dimensional structure was available for any PGP. Results: The crystal structure of pyroglutamyl peptidase I (PGP-I) from Bac illus amyloliquefaciens has been determined to 1.6 Angstrom resolution. The crystallographic asymmetric unit of PGP-I is a tetramer of four identical monomers related by noncrystallographic 222 symmetry. The protein folds int o an alpha/beta globular domain with a hydrophobic core consisting of a twi sted beta sheet surrounded by five alpha helices. The structure allows the function of most of the conserved residues in the PGP-I family to be identi fied. The catalytic triad comprises Cys144, His168 and Glu81. Conclusions: The catalytic site does not have a conventional oxyanion hole, although Cys144, the sidechain of Arg91 and the dipole of an alpha helix c ould all stabilize a negative charge. The catalytic site has an S1 pocket l ined with conserved hydrophobic residues to accommodate the pyroglutamyl re sidue. Aside from the S1 pocket, there is no clearly defined mainchain subs trate-binding region, consistent with the lack of substrate specificity. Al though the overall structure of PGP-I resembles some other alpha/beta twist ed open-sheet structures, such as purine nucleoside phosphorylase and cutin ase, there are important differences in the location and organization of th e active-site residues. Thus, PGP-I belongs to a new family of cysteine pro teases.