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

• Published in: Structure (London) Vol. 7; no. 4; pp. 399 - 411
• Main Authors: Odagaki, Y, Hayashi, A, Okada, K, Hirotsu, K, Kabashima, T, Ito, K, Yoshimoto, T, Tsuru, D, Sato, M, Clardy, J
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15-04-1999
• Subjects: Amino Acid Sequence; Bacillus - enzymology; Bacillus amyloliquefaciens; Bacterial Proteins - chemistry; Binding Sites; Biopolymers; Catalytic Domain; Crystallography, X-Ray; Cysteine Endopeptidases - chemistry; cysteine protease; Models, Molecular; Molecular Sequence Data; Protein Conformation; pyroglutamyl peptidase; Pyroglutamyl-Peptidase I - chemistry; Sequence Alignment; Sequence Homology, Amino Acid; Structure-Activity Relationship; X-ray crystallography; cysteine protease; X-ray crystallography; Bacillus amyloliquefaciens; pyroglutamyl peptidase
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/S0969-2126(99)80053-7

Background: The N-terminal pyroglutamyl (pGlu) residue of peptide hormones, such as thyrotropin-releasing hormone (TRH) and luteinizing hormone releasing hormone (LH-RH), confers resistance to proteolysis by conventional aminopeptidases. 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
Bacillus amyloliquefaciens has been determined to 1.6 Å resolution. The crystallographic asymmetric unit of PGP-I is a tetramer of four identical monomers related by noncrystallographic 222 symmetry. The protein folds into an
α/
β globular domain with a hydrophobic core consisting of a twisted
β sheet surrounded by five
α helices. The structure allows the function of most of the conserved residues in the PGP-I family to be identified. 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
α helix could all stabilize a negative charge. The catalytic site has an S1 pocket lined with conserved hydrophobic residues to accommodate the pyroglutamyl residue. Aside from the S1 pocket, there is no clearly defined mainchain substrate-binding region, consistent with the lack of substrate specificity. Although the overall structure of PGP-I resembles some other
α/
β twisted open-sheet structures, such as purine nucleoside phosphorylase and cutinase, there are important differences in the location and organization of the active-site residues. Thus, PGP-I belongs to a new family of cysteine proteases.