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.

  • Scientific Correspondence
  • Published:

Crystal structure of Escherichia coli HdeA

Nature Structural Biology volume 5, pages 763–764 (1998)Cite this article

While attempting to solve the crystal structure of cyanovirin-N1, we inadvertently obtained the structure of an unrelated Escherichia coli protein, HdeA (where Hde stands for hns-dependent expression), which we subsequently found to be the major component of the particular sample used for crystallization. Our experience may be an indication of what is to be expected when ‘structural genomics’ projects aimed at solving protein structures without regard to their function, but rather in search of new structural motifs2 will be done by design rather than by chance.

At this stage of model building, we realized that the map could not represent cyanovirin-N, especially after we analyzed the NMR-derived coordinates, which contained no helical secondary structure3. Because the identity of the protein that we had crystallized was not immediately known, we built a trial sequence based on the shapes and locations of the side chain densities. The resulting structure was subsequently refined (an Rfree of 32.0% and an R-factor of 25.5%). The presence of a cluster of three aromatic side chains, one of them clearly a tryptophan, adjacent to a disulfide bridge, together with mass spectrometry data on the crystallization sample, which showed that the main component had an Mr of 9,739.7, provided an initial indication that the structure was that of HdeA. This protein is only slightly smaller than cyanovirin-N. Further crystallographic refinement, utilizing the sequence of HdeA, resulted in a model containing 76 residues (10–85) out of 89. The N- and C-terminal residues were significantly disordered in all three molecules, and their positions could not be determined from the electron density maps. The statistics of the final refined structure are summarized in Table 1.

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: Stereo diagrams of the structure of HdeA.

References

  1. Gustafson, K.R. et al. Biochem. Biophys. Res. Commun. 238, 223–228 (1997).

    Article  CAS  Google Scholar 

  2. Shapiro, L. & Lima, C.D. Structure 6, 265–267 (1998).

    Article  CAS  Google Scholar 

  3. Bewley, C.A. et al. Nature Struct. Biol. 5, 571–578 (1998).

    Article  CAS  Google Scholar 

  4. Holm, L. & Sander, C. J. Mol. Biol. 233, 123–138 (1993).

    Article  CAS  Google Scholar 

  5. Djordjevic, S. & Stock, A.M. Structure. 5, 545–558 (1997).

    Article  CAS  Google Scholar 

  6. Yoshida, T., Ueguchi, C. & Mizuno, T. J. Bacteriol. 175, 7747–7748 (1993).

    Article  CAS  Google Scholar 

  7. Link, A.J., Phillips, D. & Church, G.M. J. Bacteriol. 179, 6228–6237 (1997).

    Article  CAS  Google Scholar 

  8. Duquerroy, S., Le Bras, G. & Janin, J. Proteins Struct. Funct. Genet. 18, 390–393 (1994).

    Article  CAS  Google Scholar 

  9. Carson, M. J. Appl. Crystallogr. 24, 958–961 (1991).

    Article  Google Scholar 

  10. Otwinowski, Z. & Minor, W. Meth. Enz.. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  11. CCP4:SERC Collaborative Computing Project No. 4. (Warrington, UK; 1979).

  12. Terwilliger, T., Kim, S.-H. & Eisenberg, D. Acta Crystallogr. A43, 1–5 (1987).

    Article  CAS  Google Scholar 

  13. Terwilliger, T.C. & Berendzen, J. Acta Crystallogr. D52, 749–757 (1996).

    CAS  Google Scholar 

  14. Brunger, A. in X-PLOR Version 3.1: A system for X-Ray crystallography and NMR (Yale University Press, New Haven, Connecticut; 1992).

  15. Jones, T.A. & Kieldgaard, M. Meth. Enz. 277, 173–208 (1997).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Clore and A. Gronenborn for the coordinates of cyanovirin-N, L.K. Pannell for mass spectrometry analysis, and A. Arthur for editorial assistance. Research sponsored in part by the National Cancer Institute, DHHS, under contract with ABL. The contents of this publication do not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

Author information

Authors and Affiliations

  1. Macromolecular Structure Laboratory, ABL-Basic Research Program, DTP, NCI-FCRDC, Frederick, 21702-1201, Maryland, USA

    Fan Yang & Alexander Wlodawer

  2. Laboratory of Drug Discovery Research and Development, DTP, NCI-FCRDC, Frederick, 21702-1201, Maryland, USA

    Kirk R. Gustafson & Michael R. Boyd

Authors
  1. Fan Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kirk R. Gustafson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael R. Boyd
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alexander Wlodawer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alexander Wlodawer.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yang, F., Gustafson, K., Boyd, M. et al. Crystal structure of Escherichia coli HdeA. Nat Struct Mol Biol 5, 763–764 (1998). https://doi.org/10.1038/1796

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/1796

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