Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Crystal structure of a novel human peroxidase enzyme at 2.0 Å resolution

Abstract

Hydrogen peroxide (H2O2) has been implicated recently as an intracellular messenger that affects cellular processes including protein phosphorylation, transcription and apoptosis. A set of novel peroxidases, named peroxiredoxins (Prx), regulate the intracellular concentration of H2O2 by reducing it in the presence of an appropriate electron donor. The crystal structure of a human Prx enzyme, HORF6, reveals that the protein contains two discrete domains and forms a dimer. The N-terminal domain has a thioredoxin fold and the C-terminal domain is used for dimerization. The active site cysteine (Cys 47), which exists as cysteine-sulfenic acid in the crystal, is located at the bottom of a relatively narrow pocket. The positively charged environment surrounding Cys 47 accounts for the peroxidase activity of the enzyme, which contains no redox cofactors.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Chae, H.Z. et al. Cloning and sequencing of thiol-specific antioxidant from mammalian brain: Alkyl hydroxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes. Proc. Natl. Acad. Sci. USA 91, 7017–7021 (1994).

    Article  CAS  Google Scholar 

  2. Chae, H.Z., Chung, S.J. & Rhee, S.G. Thioredoxin-dependent peroxide reductase from yeast. J. Biol. Chem. 269, 27670–27678 (1994).

    CAS  PubMed  Google Scholar 

  3. Netto, L E.S., Chae, H. Z., Kang, S. W., Rhee, S. G. & Stadtman, E. R. Removal of hydrogen peroxide by thiol-specific antioxidant enzyme (ISA) is involved with its antioxidant properties. J. Biol. Chem. 271, 15315–15321 (1996).

    Article  CAS  Google Scholar 

  4. Kang, S.W. et al. Role of three mammalian peroxiredoxin isoforms in receptor signaling. J. Biol. Chem. 273, 6297–6302 (1998).

    Article  CAS  Google Scholar 

  5. Jin, D.-Y., Chae, H.Z., Rhee, S.G. & Jeang, K.-T. Regulatory role for a novel human thioredoxin peroxidase in NF-KB activation. J. Biol. Chem. 272, 30952–30961 (1997).

    Article  CAS  Google Scholar 

  6. Sauri, H., Ashjian, P.H., Kim, A.T. & Shau, H. Recombinant natural killer enhancing factor augments natural killer cytotoxicity. J. Leukoc. Biol. 59, 925–931 (1996).

    Article  CAS  Google Scholar 

  7. Zhang, P. et al. Thioredoxin peroxidase is a novel inhibitor of apoptosis with a mechanism distinct from that of Bcl-2. J. Biol. Chem. 272, 30615–30618 (1997).

    Article  CAS  Google Scholar 

  8. Chae, H.Z., Uhm, T.B. & Rhee, S.G. Dimerization of thiol-specific antioxidant and the essential role of cysteine 47. Proc. Natl. Acad. Sci. USA 91, 7022–7026 (1994).

    Article  CAS  Google Scholar 

  9. Kang, S.W., Baines, I.C. & Rhee, S.G. Characterization of a mammalian peroxiredoxin that contains one conserved cysteine. J. Biol. Chem. 273, 6303–6311(1998).

    Article  CAS  Google Scholar 

  10. Kim, T.-S. et al. Identification of a human cDNA clone for lysosomal type Ca2+- independent phospholipase A2 and properties of the expressed protein. J. Biol. Chem. 272, 2542–2550 (1997).

    Article  CAS  Google Scholar 

  11. Choi, H.-J., Kang, S.W., Yang, C.-H., Rhee, S.G. & Ryu, S.-E. Crystallization and preliminary X-ray studies of hORF6, a novel human antioxidant enzyme. Acta Crystallogr. D, in the press.

  12. Poole, L.B. & Claiborne, A. The non-flavin redox center of the streptococcal NADH peroxidase. J. Biol. Chem 264, 12330–12338 (1989).

    CAS  PubMed  Google Scholar 

  13. Yeh, J.I., Claiborne, A. & Hoi, W.G.J. Structure of the cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 Å resolution. Biochemistry 35, 9951–9957 (1996).

    Article  CAS  Google Scholar 

  14. Lundblad, R.L. & Noyes, C.M. Chemical reagents for protein modification (CRC Press, Boca Raton, Florida; 1984).

    Google Scholar 

  15. Zang, Z.-Y. & Dixon, J.E. Active site labeling of the Yersinia protein tyrosine phosphatase: The determination of the pKa of the active site cysteine and the function of the conserved histidine 402. Biochemistry 32, 9340–9345 (1993).

    Article  Google Scholar 

  16. Lewis, S.D., Johnson, F.A. & Shafer, J.A. Effect of cysteine-25 on the ionization of histidine-159 in papain as determined by proton nuclear magnetic resonance spectroscopy. Biochemistry 20, 48–51 (1981).

    Article  CAS  Google Scholar 

  17. Hecht, D. & Zick, Y. Selective inhibition of protein tyrosine phosphatase activities by H2O2 and vanadate in vitro. Biochem. Biophys. Res. Comm. 188, 773–779 (1992).

    Article  CAS  Google Scholar 

  18. Sullivan, S.G. et al. Effects of H2O2 on protein tyrosine phosphatase activity in HER14 cells. Free Radical Biol. & Med. 16, 399–403 (1994).

    Article  CAS  Google Scholar 

  19. Bae, Y.S. et al. Epidermal growth factor (EGF)-induced generation of hydrogen peroxide. J. Biol. Chem. 272, 217–221 (1997).

    Article  CAS  Google Scholar 

  20. Bergdoll, M., Remy, M.-H., Cagnon, C., Masson, J.-M. & Dumas, P. Proline-dependent oligomerization with arm exchange. Structure 5, 391–401 (1997).

    Article  CAS  Google Scholar 

  21. Bennett, M.J. & Eisenberg, D. Refined structure of monomeric diphtheria toxin at 2.3 Å resolution. Prot. Sci. 3, 1464–1475 (1994).

    Article  CAS  Google Scholar 

  22. Wlodawer, A. . et al. The refined crystal structure of ribonuclease A at 2.0 A resolution. J. Biol. Chem. 257, 1325–1332 (1982).

    CAS  PubMed  Google Scholar 

  23. Martin, J.L. Thioredoxin — a fold for all reasons. Structure 3, 245–250 (1995).

    Article  CAS  Google Scholar 

  24. Epp, O., Ladenstein, R. & Wendel, A. The refined structure of the selenoenzyme glutathione peroxidase at 0.2 nm resolution Eur. J. Biochem. 133, 51–69 (1983).

    Article  CAS  Google Scholar 

  25. Ladenstein, R., Epp, O., Bartels, K., Jones, A. & Huber, R. Structure analysis and molecular model of the selenoenzyme glutathione peroxidase at 2.8 Å resolution. L. Mol. Biol. 134, 199–218 (1979).

    Article  CAS  Google Scholar 

  26. Lander, H.M. An essential role for free radicals and derived species in signal transduction. FASEB J. 11, 118–124 (1997).

    Article  CAS  Google Scholar 

  27. Collaborative Computational Project No.4.The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).

  28. Jones, Y.A. A graphical model building and refinement system for macromolecules. J. Appl. Crystallogr. 11, 268 (1978).

    Article  CAS  Google Scholar 

  29. Brunger, A.T., Kuriyan, J. & Karplus, M. R-factor refinement by molecular dynamics. Science 235, 458–460 (1987).

    Article  CAS  Google Scholar 

  30. Brunger, A.T. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr. D49, 24–36 (1993).

    CAS  Google Scholar 

  31. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–290 (1993).

    Article  CAS  Google Scholar 

  32. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  33. Merritt, E.A., Murphy, M.E.P. RASTER3D version 2.0: a program for photorealistic molecular graphics. Acta Crystallogr. D50, 869–873 (1994).

    CAS  Google Scholar 

  34. Nicholls, A. GRASP: graphical representation and analysis of surface properties.Columbia University, New York. (1993).

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Seong-Eon Ryu.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Choi, HJ., Kang, S., Yang, CH. et al. Crystal structure of a novel human peroxidase enzyme at 2.0 Å resolution. Nat Struct Mol Biol 5, 400–406 (1998). https://doi.org/10.1038/nsb0598-400

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0598-400

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing