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

Structure

Volumn 7, Issue 4, 1999, Pages 399-411

  Odagaki, Y ^a,b,e   Hayashi, A ^b   Okada, K ^b   Hirotsu, K ^b   Kabashima, T ^c   Ito, K ^c   Yoshimoto, T ^c   Tsuru, D ^c   Sato, M ^d   Clardy, J ^a  

^a and Materials Science Center   (United States)

^b Osaka City University   (Japan)

^c NAGASAKI UNIVERSITY   (Japan)

^d YOKOHAMA CITY UNIVERSITY   (Japan)

^e ONO PHARMACEUTICAL CO   (Japan)

Author keywords

Bacillus amyloliquefaciens; Cysteine protease; Pyroglutamyl peptidase; X ray crystallography

Indexed keywords

CYSTEINE PROTEINASE; PEPTIDASE;

ARTICLE; BACILLUS AMYLOLIQUEFACIENS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME ISOLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; X RAY CRYSTALLOGRAPHY;

BACILLUS AMYLOLIQUEFACIENS;

EID: 0012095492     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80053-7     Document Type: Article

References (64)

1. Doolittle, R.F. & Armentrout, R.W. (1968). Pyrrolidonyl peptidase. An enzyme for selective removal of pyrrolidonecarboxylic acid residues from polypeptides Biochemistry 7, 516-521.
2. Folkers, K., Enzmann, F., Boler J., Bowers, C.Y. & Schally, A.V. (1969). Discovery of modification of the synthetic tripeptide-sequence of the thyrotropin releasing hormone having activity. Biochem. Biophys. Res. Commun. 37, 123-126.
3. Nair, R.M.G., Barrett, J.F., Bowers, C.Y. & Schally, A.V. (1970). Structure of porcine thyrotropin releasing hormone. Biochemistry 9, 1103-1106.
4. Matsuo, H., Baba, Y., Nair, R.M.G., Arimura, A. & Schally, A.V. (1971). Structure of the porcine LH- and FSH-releasing hormone. I. The proposed amino acid sequence Biochem. Biophys. Res. Commun. 43, 1334-1339.
5. Metcalf, G. & Jackson, M.D. (1989). Thyrotropin-Releasing Hormone Biomedical Significance. New York Academy of Sciences Press, New York.
6. Shaw, R.W. (1993). The Control and Stimulation of Follicular Growth. Parthenon Publishing Group, New York.
7. Tach, Y., Melchiorri, P. & Negri, L. (1988). Bombesin-Like Peptides in Health and Disease. New York Academy of Sciences Press, New York, NY.
8. Kitabgi, P. & Nemeroff, C.B. (1992). The Neurobiology of Neurotensin. New York Academy of Sciences Press, New York.
9. Walsh, J.H. (1993). Gastrin. Raven Press, New York.
10. Awade, A.C., Cleuziat, P., Gonzales, T. & Robert-Baudouy, J. (1994). Pyrrolidone carboxyl peptidase (Pcp): An enzyme that removes pyroglutamic acid (pGlu) from pGlu-peptides and pGlu-proteins. Proteins 20, 34-51 .
11. Fujiwara, K., Kobayashi, R., Tsuru, D. (1979). The substrate specificity of pyrrolidone carboxylyl peptidase from Bacillus amyloliquefaciens. Biochem. Biophys. Acta 570, 140-148.
12. Bauer, K. & Nowak, P. (1979). Characterization of a thyroliberin-degrading serum enzyme catalyzing the hydrolysis of thyroliberin at the pyroglutamyl-histidine bond. Eur. J. Biochem. 99, 239-246.
13. Wilk, S. & Wilk, E.K. (1989). Pyroglutamyl peptidase II, a TRH degrading enzyme. Purification and specificity studies of the rabbit brain enzyme. Neurochem. Int. 15, 81-90.
14. Fuse, Y., Polk, D.H., Lam, R.W., Reviczky, A.L. & Fisher, D.A. (1990). Distribution and ontogeny of TRH-degrading enzymes in rats. Am. J. Physiol. 259, E787-E791.
15. Wilk, S. (1986). Neuropeptide-specific peptidases: Does brain contain a specific TRH-degrading enzyme? Life Sciences 39, 1487-1492.
16. Wang, J., Whetsell, M. & Klein, J.R. (1997). Local hormone networks and intestinal T cell homeostasis. Science 275, 1937-1939.
17. Yoshimoto, T., Shimoda, T., Kitazono, A., Kabashima, T., Ito, K. & Tsuru, D. (1993). Pyroglutamyl peptidase gene from Bacillus amyloliquefaciens: Cloning, sequencing, expression, and crystallization of the expressed enzyme. J. Biochem. Tokyo 113, 67-73.
18. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
19. Kahn, P. & Cameron, G. (1990). EMBL data library. Methods Enzymol. 183, 23-31.
20. Rawlings, N.D. & Barrett, A.J. (1994). Families of cysteine peptidases. Methods Enzymol. 244, 461-486.
21. Allaire, M., Chernaia, M.M., Malcolm, B.A. & James, M.N.G. (1994). Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 369, 72-76.
22. Wilson, K.P., Black, J.A., Livingston, D.J., & et al. (1994). Structure and mechanism of interleukin-1β converting enzyme. Nature 370, 270-275.
23. Walker, N.P.C., Talanian, R.V., Wong, W.W., & et al. (1994). Crystal structure of the cysteine protease interleukin-1β-converting enzyme: A (p20/p10)2 homodimer. Cell 78, 343-352.
24. Ding, J., McGrath. W.J., Sweet. R.M. & Mangel, W.F. (1996). Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor. EMBO J. 15, 1778-1783.
25. Brändén, C.I. (1980). Relation between structure and function of α/β proteins. Q. Rev. Biophys. 13, 317-338.
26. Brändén, C. & Tooze, J. (1991). Introduction to Protein Structure. Garland Publishing, Inc. New York, USA.
27. Le Saux, O., Gonzales, T. & Robert-Baudouy, J. (1996). Mutational analysis of the active site of Pseudomonas fluorescens pyrrolidone carboxyl peptidase. J. Bacteriol. 178, 3308-3313.
28. Nicholls, A.J. (1993). GRASP Manual. Columbia University, New York, USA.
29. Szewczuk, A. & Mulczyk, M. (1969). Pyrrolidonyl peptidase in bacteria. The enzyme from Bacillus subtilis. Eur. J. Biochem. 8, 63-67.
30. Gonzales T., Awade A., Besson, C. & Robert-Baudouy, J. (1992). Purification and characterization of recombinant pyrrolidone carboxyl peptidase of Bacillus subtilis, J. Chromatogr. Biomed. Applic. 584, 101-107.
31. Awade, A., Cleuziat, P., Gonzales, T. & Robert-Baudouy, J. (1992). Characterization of the pcp gene encoding the pyrrolidone carboxyl peptidase of Bacillus subtilis. FEBS Lett. 305, 67-73.
32. Lauffart, B., McDermott, J.R., Biggins, J.A., Gibson, A.M. & Mantle, D. (1988). Purification and characterization of pyroglutamyl aminopeptidase from human cerebral cortex. Biochem. Soc. Trans. 17, 207-208.
33. Mantle, D., Lauffart, B., McDermott, J.R. & Gibson, A.M. (1990). Characterization of aminopeptidases in human kidney soluble fraction. Clin. Chim. Acta 187, 105-113.
34. Mantle, D., Lauffart, B. & Gibson, A. (1991). Purification and characterization of leucyl aminopeptidase and pyroglutamyl aminopeptidase from human skeletal muscle. Clin. Chim. Acta 197, 35-45.
35. Fujinaga, M., Chernaia, M.M., Halenbeck, R., Koths, K. & James, M.N.G. (1996). The crystal structure of PR3, a neutrophil serine proteinase antigen of Wegener's granulomatosis antibodies. J. Mol. Biol. 261, 267-278.
36. Pereira, P.J.B., Bode, W. & et al.(1998). Human β-tryptase is a ring- like tetramer with active sites facing a central pore. Nature 392, 306-311.
37. Doran, J.D. & Carey, P.R. (1996). α-Helix dipoles and catalysis: Absorption and Raman spectroscopic studies of acyl cysteine proteases. Biochemistry 35, 12495-12502.
38. Henderson, R. (1970). Structure of crystalline α-chymotrypsin. IV. The structure of indoleacryloyl-α-chymotrypsin and its relevance to the hydrolytic mechanism of the enzyme. J. Mol. Biol. 54, 341-354.
39. Warshel, A. & Russell, S. (1986). Theoretical correlation of structure and energetics in the catalytic reaction of trypsin. J. Am. Chem. Soc. 108, 6569-6579.
40. Asboth, B. & Polgar, L. (1983). Transition-state stabilization at the oxyanion binding sites of serine and thiol proteinases: Hydrolyses of thiono and oxygen esters. Biochemistry 22, 117-122.
41. Menard, R., et al., & Storer, A.C. (1991). Contribution of the glutamine 19 side chain to transition-state stabilization in the oxyanion hole of papain. Biochemistry 30, 8924-8928.
42. Charmm/QUANTA. (1997). San Diego: Molecular Simulations Inc.
43. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
44. Narayana, S.V.L., Bugg, C.E. & Ealick, S.E. (1997). Refined structure of purine nucleoside phosphorylase at 2.75 Å resolution. Acta Crystallogr. D53, 131-142.
45. Martinez, C., De Geus, P., Lauwereys, M., Matthyssens, G. & Cambillau, C. (1992). Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent. Nature 356, 615-618.
46. Jancarik, J. & Kim, S.H. (1991 ). Sparse matrix sampling: A screening method for crystallization of proteins. J. Appl. Crystallogr. 24, 409-411.
47. Howard, A.J., Nielsen, C. & Xuong, N.H. (1985). Software for a diffractometer with multiwire area detector. Methods Enzymol. 114, 452-472.
48. Xuong, N.H., Nielsen, C., Hamlin, R. & Anderson, D. (1985). Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer. J. Appl. Crystallogr. 18, 342-350.
49. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 A, 307-326.
50. Furey, W. & Swaminathan, S. (1995). PHASES-95: A Program Package for the Processing and Analysis of Diffraction Data from Macromolecules. University of Pittsburgh, Pittsburgh, PA.
51. Collaborative Computational Project No. (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
52. Sack, J.S. (1988). CHAIN - a crystallographic modeling program. J. Mol. Biol. 6, 224-225.
53. Brünger, AT. (1992). X-PLOR Manual, Version 3.1. Yale University Press, New Haven, CT, USA.
54. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
55. Cleuziat, P., Awade A. & Robert-Baudouy, J. (1992). Molecular characterization of pcp, the structural gene encoding the pyrrolidone carboxylyl peptidase from Streptococcus pyrogenes. Mol. Microbiol. 6, 2051-2063.
56. Daveran-Mingot, M.L., Campo, N., Ritzenthaler, P. & Le Bourgeois, P. (1998). A natural large chromosomal inversion in Lactococcus lactis is mediated by homologous recombination between two insertion sequence. J. Bacteriol. 180, 4834-4842.
57. Patti, J.M., Schneider, A., Garza, N. & Boles, J.O. (1995). Isolation and characterization of pcp, a gene encoding a pyrrolidone carboxyl peptidase in Staphylococcus aureus. Gene 166, 95-99.
58. Gonzales, T. & Robert-Baudouy, J. (1994). Characterization of the pcp gene of Pseudomonas fluorescens and of its product, pyrrolidone carboxyl peptidase (Pcp). J. Bacteriol. 176, 2569-2576.
59. Kawarabayashi, Y., Sawada, M., et al. & Kikuchi, H. (1998). Complete sequence and gene organization of the genome of a hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5, 55-76.
60. Bowman, S., Churcher, C., et al., & Barrel, B. (1997). The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII. Nature 387 Supplement, 90-93.
61. Tsunasawa, S., Nakura, S., Tanihawa, T. & Kato, I. (1998). Pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Pyrococcus furisus: Cloning and overexpression in Escherichia coli of the gene, and its application to protein sequence analysis. J. Biochem. 124, 778-783.
62. Kraulis, P.J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
63. Merritt, E.A. & Murphy, M.E.P. (1994). Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869-873.
64. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these methods. Acta Crystallogr. A 47, 110-119.