PDBsum entry 1aug

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Thiol protease PDB id
Protein chains
210 a.a. *
Waters ×315
* Residue conservation analysis
PDB id:
Name: Thiol protease
Title: Crystal structure of the pyroglutamyl peptidase i from bacillus amyloliquefaciens
Structure: Pyroglutamyl peptidase-1. Chain: a, b, c, d. Synonym: pgp-1, pyrrolidone-carboxylate peptidase. Engineered: yes
Source: Bacillus amyloliquefaciens. Organism_taxid: 1390. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
2.00Å     R-factor:   0.197     R-free:   0.259
Authors: Y.Odagaki,A.Hayashi,K.Okada,K.Hirotsu,T.Kabashima,K.Ito, T.Yoshimoto,D.Tsuru,M.Sato,J.Clardy
Key ref:
Y.Odagaki et al. (1999). The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease. Structure, 7, 399-411. PubMed id: 10196127 DOI: 10.1016/S0969-2126(99)80053-7
26-Aug-97     Release date:   23-Mar-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P46107  (PCP_BACAM) -  Pyrrolidone-carboxylate peptidase
215 a.a.
210 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Pyroglutamyl-peptidase I.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 5-oxoprolyl-peptide + H2O = 5-oxoproline + peptide

Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1016/S0969-2126(99)80053-7 Structure 7:399-411 (1999)
PubMed id: 10196127  
The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease.
Y.Odagaki, A.Hayashi, K.Okada, K.Hirotsu, T.Kabashima, K.Ito, T.Yoshimoto, D.Tsuru, M.Sato, J.Clardy.
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 A 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 alpha/beta globular domain with a hydrophobic core consisting of a twisted 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 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 alpha 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 alpha/beta 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.
  Selected figure(s)  
Figure 7.
Figure 7. Comparisons of PGP-I with related structures. (a) Ribbon diagrams of PGP-I and PNP. (b) Ribbon diagrams of PGP-I and cutinase. The regions of topological consensus are shown in red and regions lacking topological consensus are shown in gray. The catalytic residues are shown in ball-and-stick representation (see text for full discussion).
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 399-411) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17119851 Z.Kilbane, P.R.Vaas, P.O.Cuív, and B.O'Connor (2007).
Cloning and heterologous expression of bovine pyroglutamyl peptidase type-1 in Escherichia coli: purification, biochemical and kinetic characterisation.
  Mol Cell Biochem, 297, 189-197.  
14709911 K.Abe, F.Saito, M.Yamada, and T.Tokui (2004).
Pyroglutamyl aminopeptidase I, as a drug metabolizing enzyme, recognizes xenobiotic substrates containing L-2-oxothiazolidine-4-carboxylic acid.
  Biol Pharm Bull, 27, 113-116.  
14600395 K.Abe, N.Watanabe, T.Kosaka, M.Yamada, T.Tokui, and T.Ikeda (2003).
Hydrolysis of synthetic substrate, L-pyroglutamyl p-nitroanilide is catalyzed solely by pyroglutamyl aminopeptidase I in rat liver cytosol.
  Biol Pharm Bull, 26, 1528-1533.  
11389725 K.Ogasahara, N.N.Khechinashvili, M.Nakamura, T.Yoshimoto, and K.Yutani (2001).
Thermal stability of pyrrolidone carboxyl peptidases from the hyperthermophilic Archaeon, Pyrococcus furiosus.
  Eur J Biochem, 268, 3233-3242.  
11410277 T.Kabashima, Y.Li, N.Kanada, K.Ito, and T.Yoshimoto (2001).
Enhancement of the thermal stability of pyroglutamyl peptidase I by introduction of an intersubunit disulfide bond.
  Biochim Biophys Acta, 1547, 214-220.  
10681429 T.F.Kagawa, J.C.Cooney, H.M.Baker, S.McSweeney, M.Liu, S.Gubba, J.M.Musser, and E.N.Baker (2000).
Crystal structure of the zymogen form of the group A Streptococcus virulence factor SpeB: an integrin-binding cysteine protease.
  Proc Natl Acad Sci U S A, 97, 2235-2240.
PDB code: 1dki
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.