Skip to main content
SpringerLink
Log in

The X-ray crystal structure of pyrrolidone–carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii

  • Published:
Journal of Structural and Functional Genomics

Abstract

The crystal structure of pyrrolidone–carboxylate peptidase (PCP) from hyperthermophilic archaea Pyrococcus horikoshii (PhoPCP) has been determined at 1.6-A resolution by X-ray crystallography. PCP belongs to the C15 family of cysteine protease, and specifically removes the amino terminal pyroglutamate residue from a wide range of N-terminal-blocking peptides. The crystal structure is very similar to that of other hyperthermophiles, Pyrococcus friosus and Thermococcus litoralis, and even that from the mesophile, Bacillus amyloliquefacience. The inter-subunit disulfide bonds, which have been proposed as one of the thermostabilizing factors of the PCP from such hyperthermophiles, was not present in PhoPCP. The result suggests that the thermostability of PhoPCP may be obtained by the accumulation of many weak factors. Abbreviations: NCS – non-crystallographic symmetry; PCP – pyrrolidone-carboxylate peptidase; rmsd – root mean square deviation

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Doolittle, R.F., and Armentrout, R.W. (1968) Biochemistry 7, 516–521. medline+5644127

    Google Scholar 

  2. Fujiwara, K., Kobayashi, R., and Tsuru, D. (1979) Biochim. Biophys. Acta 570, 140–148. medline+39608

    Google Scholar 

  3. Uliana, J.A., and Doolittle, R.F. (1969) Arch. Biochem. Biophys. 131, 561–565. medline+5787224

    Google Scholar 

  4. Awade, A.C., Cleuziat, P., Gonzales, T., and Robert-Baudouy, J. (1994) Proteins. 20, 34–51. medline+7824521

    Google Scholar 

  5. Cummins, P.M., and O'Connor, B. (1998) Biochim. Biophys. Acta 1429, 1–17. medline+9920379

    Google Scholar 

  6. Folkers, K., Enzmann, F., Boler, J., Bowers, C.Y., and Schally, A.V. (1969) Biochem. Biophys. Res. Commun. 37, 123–126. medline+4981343

    Google Scholar 

  7. Nair, R.M., Barrett, J.F., Bowers, C.Y., and Schally, A.V. (1970) Biochemistry. 9, 1103–1106.

    Google Scholar 

  8. Matsuo, H., Baba, Y., Nair, R.M., Arimura, A., and Schally, A.V. (1971) Biochem. Biophys. Res. Commun. 43, 1334–1339.

    Google Scholar 

  9. Barelli, H., Vincent, J.P., and Checler, F. (1988) Eur. J. Biochem. 175, 481–489. medline+3409880

    Google Scholar 

  10. Carver, J.A., and Collins, J.G. (1990) Eur. J. Biochem. 187, 645–650. medline+2303058

    Google Scholar 

  11. Tanaka, H., Chinami, M., Mizushima, T., Ogasahara, K., Ota, M., Tsukihara, T., and Yutani, K. (2001) J. Biochem. 130, 107–118. PDB+1IOF, medline+11432786

    Google Scholar 

  12. Singleton, M., Isupov, M., and Littlechild, J. (1999) Structure Fold Des. 7, 237–244. PDB+1A2Z, medline+10368293

    Google Scholar 

  13. Singleton, M.R., and Littlechild, J.A. (2001) Methods Enzymol. 330, 394–403. medline+11210517

    Google Scholar 

  14. Odagaki, Y., Hayashi, A., Okada, K., Hirotsu, K., Kabashima, T., Ito, K., Yoshimoto, T., Tsuru, D., Sato, M., and Clardy, J. (1999) Structure Fold Des. 7, 399–411. PDB+1AUG, medline+

    Google Scholar 

  15. Ito, K., Inoue, T., Takahashi, T., Huang, H.S., Esumi, T., Hatakeyama, S., Tanaka, N., Nakamura, K.T., and Yoshimoto, T. (2001) J. Biol. Chem. 276, 18557–18562. medline+

    Google Scholar 

  16. Ogasahara, K., Khechinashvili, N.N., Nakamura, M., Yoshimoto, T., and Yutani, K. (2001) Eur. J. Biochem. 268, 3233–3242. medline+11389725

    Google Scholar 

  17. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S., Sekine, M., Baba, S., Kosugi, H., Hosoyama, A., Nagai, Y., Sakai, M., Ogura, K., Otsuka, R., Nakazawa, H., Takamiya, M., Ohfuku, Y., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., and Kikuchi, H. (1998) DNA Res. 5, 55–76. medline+

    Google Scholar 

  18. Leslie, A.G.W. (1994) MOSFLM Users Guide, MRC-LMB, Cambridge, England.

    Google Scholar 

  19. Number 4 Collaborative Computional Project. (1994) Acta Crystallogr. D50, 760–763.

    Google Scholar 

  20. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard. (1991) Acta Crystallogr. A47, 110–119. medline+2025413

    Google Scholar 

  21. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L. (1998) Acta Crystallogr. D54, 905–921. medline+9757107

    Google Scholar 

  22. Genoscope. (http: //www.genoscope.cns.fr/pab/)

  23. Le Saux, O., Gonzales, T., and Robert-Baudouy, J. (1996) J. Bacteriol. 178, 3308–3313. medline+8655512

    Google Scholar 

  24. Watanabe, K., Hata, Y., Kizaki, H., Katsube, Y., and Suzuki, Y. (1997) J. Mol. Biol. 269, 142–153. medline+9193006

    Google Scholar 

  25. Rawlings, N.D., and Barrett, A.J. (1994) Methods Enzymol. 244, 461–486. medline+7845226

    Google Scholar 

  26. Yoshimoto, T., Shimoda, T., Kitazono, A., Kabashima, T., Ito, K., and Tsuru, D. (1993) J. Biochem. 113, 67–73. medline+

    Google Scholar 

  27. Gonzales, T., Awade, A., Besson, C., and Robert-Baudouy, J. (1992) J. Chrom. 584, 101–107.

    Google Scholar 

  28. Kabashima, T., Li, Y., Kanada, N., Ito, K., and Yoshimoto, T. (2001) Biochim. Biophys. Acta 1547, 214–220. medline+

    Google Scholar 

  29. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1992) J. Appl. Crystallogr. 26, 283–291.

    Google Scholar 

  30. Singleton, M.R., Parratt, J.S., Taylor, S.J.C., and Littlechild, J.A. (2000) Extremophiles. 4, 297–303. medline+11057915

    Google Scholar 

  31. Tsunasawa, S., Nakura, S., Tanigawa, T., and Kato, I. (1998) J. Biochem. 124, 778–783. medline+9756623

    Google Scholar 

  32. Parkhill, J., Wren, B.W., Thomson, N.R., Titball, R.W., Holden, M.T., Prentice, M.B., Sebaihia, M., James, K.D., Churcher, C., Mungall, K.L., Baker, S., Basham, D., Bentley, S.D., Brooks, K., Cerdeno-Tarraga, A.M., Chillingworth, T., Cronin, A., Davies, R.M., Davis, P., Dougan, G., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Karlyshev, A.V., Leather, S., Moule, S., Oyston, P.C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S., and Barrell, B.G. (2001) Nature. 413, 523–527. medline+11586360

    Google Scholar 

  33. Gonzales, T., and Robert-Baudouy, J. (1994) J. Bacteriol. 176, 2569–2576. medline+7909543

    Google Scholar 

  34. Awade, A.C., Cleuziat, P., Gonzales, T., and Robert-Baudouy, J. (1992) FEBS Lett. 305, 67–73. medline+1353026

    Google Scholar 

  35. Cleuziat, P., Awade, A., and Robert-Baudouy, J. (1992) J. Mol. Microbiol. 6, 2051–2063. medline+1357525

    Google Scholar 

  36. Takami, H., Nakasone, K., Takaki, Y., Maeno, G., Sasaki, R., Masui, N., Fuji, F., Hirama, C., Nakamura, Y., Ogasawara, N., Kuhara, S., and Horikoshi, K. (2000) Nucleic Acids Res. 28, 4317–4331. medline+11058132

    Google Scholar 

  37. Daveran-Mingot, M.L., Campo, N., Ritzenthaler, P., and Le Bourgeois, P. (1998) J. Bacteriol. 180, 4834–4842. medline+

    Google Scholar 

  38. She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M.J., Chan-Weiher, C.C., Clausen, I.G., Curtis, B.A., De Moors, A., Erauso, G., Fletcher, C., Gordon, P.M., Heikamp-de Jong, I., Jeffries, A.C., Kozera, C.J., Medina, N., Peng, X., Thi-Ngoc, H.P., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R.L., Doolittle, W.F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M.A., Sensen, C.W., and Van der Oost, J. (2001) Proc. Natl. Acad. Sci. USA 98, 7835–7840. medline+11427726

    Google Scholar 

  39. Patti, J.M., Schneider, A., Garza, N., and Boles, J.O. (1995) Gene 166, 95–99. medline+8529900

    Google Scholar 

  40. Vriend, G. (1990) J. Mol. Graph. 8, 52–56.

    Google Scholar 

  41. Kraulis, P.J. (1991) J. Appl. Crystallogr. 24, 946–950.

    Google Scholar 

  42. Merrit, E.A., and Murphy, M.E.P. (1994) Acta Crystallogr. D50, 869–873.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan

    Masaaki Sokabe, Takashi Kawamura, Naoki Sakai, Min Yao, Nobuhisa Watanabe & Isao Tanaka

Authors
  1. Masaaki Sokabe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Takashi Kawamura
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Naoki Sakai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Min Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nobuhisa Watanabe
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Isao Tanaka
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sokabe, M., Kawamura, T., Sakai, N. et al. The X-ray crystal structure of pyrrolidone–carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii. J Struct Func Genom 2, 145–154 (2002). https://doi.org/10.1023/A:1021257701676

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1021257701676

Search

Navigation