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.

  • Letter
  • Published:

Cellvibrio japonicus α-L-arabinanase 43A has a novel five-blade β-propeller fold

Nature Structural Biology volume 9, pages 665–668 (2002)Cite this article

Abstract

Cellvibrio japonicus arabinanase Arb43A hydrolyzes the α-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The three-dimensional structure of Arb43A, determined at 1.9 Å resolution, reveals a five-bladed β-propeller fold. Arb43A is the first enzyme known to display this topology. A long V-shaped surface groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Comparison of the three-dimensional structure of Arb43A and tachylectin.
Figure 2: The reaction catalyzed by Arb43A.
Figure 3: Three-dimensional structure of Arb43A in complex with substrate.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Bacic, A., Harris, P.J. & Stone, B.A. in The Biochemistry of Plants Vol. 14 (ed. Preiss, J.) 297–371 (Academic Press, San Diego; 1988).

    Book  Google Scholar 

  2. Matsuo, N., Kaneko, S., Kuno, A., Kobayashi, H. & Kusakabe, I. Biochem. J. 346, 9–15 (2000).

    Article  CAS  Google Scholar 

  3. McKie, V.A. et al. Biochem. J. 323, 547–555 (1997).

    Article  CAS  Google Scholar 

  4. Coutinho, P.M. & Henrissat, B. in Recent Advances in Carbohydrate Engineering (eds Gilbert, H.J., Davies, G.J., Svensson, B. & Henrissat, B.) 3–12 (Royal Society of Chemistry, Cambridge, UK; 1999).

    Google Scholar 

  5. Nagy, T., Emami, K., Fontes, C.M.G.A., Ferreira, L.M.A. & Gilbert, H.J. J. Bacteriol. 184, 4925–4929 (2002).

    Article  CAS  Google Scholar 

  6. Fülöp, V. & Jones, D.T. Curr. Opin. Struct. Biol. 9, 715–721 (1999).

    Article  Google Scholar 

  7. Baker, S.C. et al. J. Mol. Biol. 269, 440–455 (1997).

    Article  CAS  Google Scholar 

  8. Neer, E.J. & Smith, T.F. Cell 84, 175–178 (1996).

    Article  CAS  Google Scholar 

  9. Beisel, H.G., Kawabata, S., Iwanaga, S., Huber, R. & Bode, W. EMBO J. 18, 2313–2322 (1999).

    Article  CAS  Google Scholar 

  10. Jawad, Z. & Paoli, M. Structure 10, 447–454 (2002).

    Article  CAS  Google Scholar 

  11. Fülöp, V., Bocskei, Z. & Polgar, L. Cell 94, 161–170 (1998).

    Article  Google Scholar 

  12. Paoli, M. Nature Struct. Biol. 8, 744 (2001).

  13. Pitson, S.M., Voragen, A.G. & Beldman, G. FEBS Lett. 398, 7–11 (1996).

    Article  CAS  Google Scholar 

  14. Davies, G., Sinnott, M.L. & Withers, S.G. in Comprehensive Biological Catalysis Vol. 1 (ed. Sinnott, M.L.) 119–209 (Academic Press, London; 1997).

    Google Scholar 

  15. Nurizzo, D., Nagy, T., Gilbert, H.J. & Davies, G.J. Structure 10, 547–556 (2002).

    Article  CAS  Google Scholar 

  16. Davies, G. & Henrissat, B. Structure 3, 853–859 (1995).

    Article  CAS  Google Scholar 

  17. Pages, S., Kester, H.C., Visser, J. & Benen, J.A. J. Biol. Chem. 276, 33652–33656 (2001).

    Article  CAS  Google Scholar 

  18. Paoli, M. Prog. Biophys. Mol. Biol, 76, 103–130 (2001).

    Article  CAS  Google Scholar 

  19. Charnock, S.J. et al. Biochemistry 39, 5013–5021 (2000).

    Article  CAS  Google Scholar 

  20. Otwinowski, Z. & Minor Methods Enzymol. 276 307–326 (1997).

    Article  CAS  Google Scholar 

  21. Terwilliger, T.C. & Berendzen, J. Acta Crystallogr. D 55, 849–861 (1999).

    Article  CAS  Google Scholar 

  22. de La Fortelle, E. & Bricogne, G. Methods Enzymol. 276, 472–494 (1997).

    Article  CAS  Google Scholar 

  23. Navaza, J. & Saludijan, P. Methods Enzymol. 276, 581–594 (1997).

    Article  CAS  Google Scholar 

  24. Cowtan, K.D. & Main, P. Acta Crystallogr.D 49, 148–157 (1996).

    Article  Google Scholar 

  25. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Acta Crystallogr D 53, 240–255 (1997).

    Article  CAS  Google Scholar 

  26. Esnouf, R.M. J. Mol. Graph. 15, 133–138 (1997).

    Google Scholar 

  27. Sharp, K., Fine, R. & Honig, B. Science 236, 1460–1463 (1987).

    Article  CAS  Google Scholar 

  28. Read, R.J. Acta Crystallogr. A 42, 140–149 (1986).

    Article  Google Scholar 

  29. Kleywegt, G.J. & Jones, T.A. Structure 4, 1395–1400 (1996).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the BBSRC and the Wellcome Trust for funding and the staff of the Daresbury and European Synchrotron Radiation Sources for provision of beamtime. D.N. thanks EMBO for provision of a long-term fellowship and G.J.D is a Royal Society University Research Fellow.

Author information

Author notes

  1. Simon J. Charnock

    Present address: School of Applied and Molecular Sciences, Northumbria University, The Ellison Building, Newcastle upon Tyne, NE1 8ST, UK

Authors and Affiliations

  1. Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, YO10 5DD, York, UK

    Didier Nurizzo, Johan P. Turkenburg, Simon J. Charnock, Shirley M. Roberts, Eleanor J. Dodson & Gideon J. Davies

  2. Department of Biological and Nutritional Sciences University of Newcastle upon Tyne, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, UK

    Vincent A. McKie, Edward J. Taylor & Harry J. Gilbert

Authors
  1. Didier Nurizzo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Johan P. Turkenburg
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Simon J. Charnock
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shirley M. Roberts
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Eleanor J. Dodson
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vincent A. McKie
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Edward J. Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Harry J. Gilbert
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Gideon J. Davies
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gideon J. Davies.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nurizzo, D., Turkenburg, J., Charnock, S. et al. Cellvibrio japonicus α-L-arabinanase 43A has a novel five-blade β-propeller fold. Nat Struct Mol Biol 9, 665–668 (2002). https://doi.org/10.1038/nsb835

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb835

This article is cited by

Search

Advanced 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