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E. coli aconitase B structure reveals a HEAT-like domain with implications for protein–protein recognition

Nature Structural Biology volume 9, pages 447–452 (2002)Cite this article

Abstract

The major bifunctional aconitase of Escherichia coli (AcnB) serves as either an enzymic catalyst or a mRNA-binding post-transcriptional regulator, depending on the status of its iron–sulfur cluster. AcnB represents a large, distinct group of Gram-negative bacterial aconitases that have an altered domain organization relative to mitochondrial aconitase and other aconitases. Here the 2.4 Å structure of E. coli AcnB reveals a high degree of conservation at the active site despite its domain reorganization. It also reveals that the additional domain, characteristic of the AcnB subfamily, is a HEAT-like domain, implying a role in protein–protein recognition. This domain packs against the remainder of the protein to form a tunnel leading to the aconitase active site, potentially for substrate channeling.

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Figure 1: The structure of AcnB.
Figure 2: Sequence alignment of E. coli AcnB and bovine mAcn with secondary-structural elements of AcnB.
Figure 3: The active site of AcnB.
Figure 4: The novel HEAT-like domain of AcnB.

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References

  1. Robbins, A.H. & Stout, C.D. Proteins Struct. Funct. Genet. 5, 289–312 (1989).

    Article  CAS  Google Scholar 

  2. Gruer, M.J., Artymiuk, P.J. & Guest, J.R. Trends Biochem. Sci. 22, 3–6 (1997).

    Article  CAS  Google Scholar 

  3. Bradbury, A.J., Gruer, M.J., Rudd, K.E. & Guest, J.R. Microbiology 142, 389–400 (1996).

    Article  CAS  Google Scholar 

  4. Cunningham, L., Gruer, M.J. & Guest, J.R. Microbiology 143, 3795–3805 (1997).

    Article  CAS  Google Scholar 

  5. Beinert, H. & Kennedy, M.C. FASEB J. 7, 1442–1449 (1993).

    Article  CAS  Google Scholar 

  6. Hentze, M.M. & Kühn, L.C. Proc. Natl. Acad. Sci. USA 93, 8175–8182 (1996).

    Article  CAS  Google Scholar 

  7. Alén, C. & Sonenshein, A.L. Proc. Natl. Acad. Sci. USA 96, 10412–10417 (1999).

    Article  Google Scholar 

  8. Tang, Y. & Guest, J.R. Microbiology 145, 3069–3079 (1999).

    Article  CAS  Google Scholar 

  9. Tang, Y., Quail, M.A., Artymiuk, P.J., Guest, J.R. & Green, J. Microbiology 148, 1027–1037 (2002).

    Article  CAS  Google Scholar 

  10. Butt, J. et al. Proc. Natl. Acad. Sci. USA 93, 4345–4349 (1996).

    Article  CAS  Google Scholar 

  11. Todd, A.E., Orengo, C.A. & Thornton, J.M. J. Mol. Biol. 307, 1113–1143 (2001).

    Article  CAS  Google Scholar 

  12. Polekhina, G., Board, P.G., Gali, R.R., Rossjohn, J. & Parker, M.W. EMBO J. 18, 3204–3213 (1999).

    Article  CAS  Google Scholar 

  13. Lauble, H., Kennedy, M.C., Beinert, H. & Stout, C.D. Biochemistry 31, 2735–2748 (1992).

    Article  CAS  Google Scholar 

  14. Lauble, H., Kennedy, M.C., Beinert, H. & Stout, C.D. J. Mol. Biol. 237, 437–451 (1994).

    Article  CAS  Google Scholar 

  15. Beinert, H., Kennedy, M.C. & Stout, C.D. Chem. Rev. 96, 2335–2373 (1996).

    Article  CAS  Google Scholar 

  16. Grindley, H.M., Artymiuk, P.J., Rice, D.W. & Willett, P. J. Mol. Biol. 229, 707–721 (1993).

    Article  CAS  Google Scholar 

  17. Groves, M.R., Hanlon, N., Turowski, P., Hemmings, B.A. & Barford, D. Cell 96, 99–110 (1999).

    Article  CAS  Google Scholar 

  18. Conti, E., Uy, M., Leighton, L., Blobel, G. & Kuriyan, J. Cell 94, 193–204 (1998).

    Article  CAS  Google Scholar 

  19. Andrade, M.A., Petosa, C., O'Donoghue, S.I., Muller, C.W. & Bork, P. J. Mol. Biol. 309, 1–18 (2001).

    Article  CAS  Google Scholar 

  20. Edwards, T.A., Pyle, S.E., Wharton, R.P. & Aggarwal, A.K. cell 105, 281–289 (2001).

    Article  CAS  Google Scholar 

  21. Wang, X.Q., Zamore, P.D. & Hall, T.M.T. Mol. Cell 7, 855–865 (2001).

    Article  CAS  Google Scholar 

  22. Wharton, R.P., Sonoda, J., Lee, T., Patterson, M. & Murata, Y. Mol. Cell 1, 863–872 (1998).

    Article  CAS  Google Scholar 

  23. Basilion, J.P., Rouault, T.A., Massinople, C.M., Klausner, R.D. & Burgess, W.H. Proc. Natl. Acad. Sci. USA 91, 574–578 (1994).

    Article  CAS  Google Scholar 

  24. Addess, K.J., Basilion, J.P., Klausner, R.D., Rouault, T.A. & Pardi, A. J. Mol. Biol. 274, 72–83 (1997).

    Article  CAS  Google Scholar 

  25. Kaldy, P., Menotti, E., Moret, R. & Kühn, L.C. EMBO J. 18, 6073–6083 (1999).

    Article  CAS  Google Scholar 

  26. Ruediger, R. et al. Mol. Cell. Biol. 12, 4872–4882 (1992).

    Article  CAS  Google Scholar 

  27. Jordan, P.A., Tang, Y., Bradbury, A., Thomson, A.J. & Guest, J.R. Biochem. J. 344, 739–746 (1999).

    Article  CAS  Google Scholar 

  28. Hyde, C.C., Ahmed, S.A., Padlan, E.A., Miles, E.W. & Davies, D.R. J. Biol. Chem. 263, 17857–17871 (1988).

    CAS  PubMed  Google Scholar 

  29. Thoden, J.B., Holden, H.M., Wesenberg, G., Raushel, F.M. & Rayment, I. Biochemistry 36, 6305–6316 (1997).

    Article  CAS  Google Scholar 

  30. Srere, P.A. Trends Biochem. Sci. 10, 109–110 (1985).

    Article  Google Scholar 

  31. Srere, P.A. Annu. Rev. Biochem. 56, 89–124 (1987).

    Article  CAS  Google Scholar 

  32. Barnes, S.J. & Weitzman, P.D.J. FEBS Lett. 201, 267–271 (1986).

    Article  CAS  Google Scholar 

  33. Nguyen, N.T. et al. Biochemistry 40, 13177–13187 (2001).

    Article  CAS  Google Scholar 

  34. Hurley, J.H. et al. Proc. Natl. Acad. Sci. USA 86, 8635–8639 (1989).

    Article  CAS  Google Scholar 

  35. Gruer, M.J., Bradbury, A.J. & Guest, J.R. Microbiology 143, 1837–1846 (1997).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  37. Bailey, S. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  38. Cowtan, K. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34–38 (1994).

  39. Roussel, A. & Cambillau, C. Silicon Graphics Geometry Partners Directory 86, 86 (1991).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  41. Brunger, A.T. Acta Crystallogr. D 49, 24–36 (1993).

    Article  CAS  Google Scholar 

  42. Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. J. Mol. Graph. 6, 13–27 (1988).

    Article  CAS  Google Scholar 

  43. Barton, G.L. Protein Eng. 6, 13–27 (1993).

    Article  Google Scholar 

  44. Esnouf, R.M. J. Mol. Graph. 15, 132–134 (1997).

    Article  CAS  Google Scholar 

  45. Nicholls, A., Bharadwaj, R. & Honig, B. Biophys. J. 64, 166 (1993).

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Acknowledgements

We thank BBSRC, EPSRC and the Wellcome Trust for their support, CCLRC Daresbury for synchrotron radiation facilities, and the Royal Society and Wolfson Foundation for computing facilities. The Krebs Institute is a BBSRC-designated Biomolecular Sciences center and a member of the North of England Structural Biology Centre.

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  1. Krebs Institute for Biomolecular Research Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK

    Colin H. Williams, Timothy J. Stillman, Vladimir V. Barynin, Svetlana E. Sedelnikova, Yue Tang, Jeffrey Green, John R. Guest & Peter J. Artymiuk

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  1. Colin H. Williams
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Correspondence to Peter J. Artymiuk.

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Williams, C., Stillman, T., Barynin, V. et al. E. coli aconitase B structure reveals a HEAT-like domain with implications for protein–protein recognition. Nat Struct Mol Biol 9, 447–452 (2002). https://doi.org/10.1038/nsb801

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