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The domain structure of the ion channel-forming protein colicin Ia

Nature Structural Biology volume 1, pages 597–604 (1994)Cite this article

Abstract

Colicin Ia undergoes a transition from a soluble to a transmembrane state, forming an ion channel to effect its bactericidal activity. The X-ray crystal structure of soluble colicin Ia at an effective resolution of 4 Å reveals that the molecule is highly α-helical and has an unusually elongated ‘Y’-shape. The stalk and two arms of the ‘Y’ form three discrete structural domains which most likely correspond to the three functional regions identified for the channel-forming colicins. The channel-forming region of colicin Ia can be located to the larger of the two arms, the insertion domain, by its structural similarity to the ten α-helix motif found for the ion channel-forming fragments of colicins A and E1. The domain arrangement found in this structure provides novel insights into the mechanism of membrane insertion of colicin Ia.

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References

  1. Pugsley, A.P. Obligatory coupling of colicin release and lysis in mitomycin-treated Col+Escherichia coli J. gen. Microbiol. 129, 1921–1928 (1983).

    CAS  PubMed  Google Scholar 

  2. Bowles, L.K., Miguel, A.G. & Konisky, J. Purification of the colicin I receptor. J. biol. Chem. 258, 1215–1220 (1983).

    CAS  PubMed  Google Scholar 

  3. Griggs, D.W., Tharp, B.B. & Konisky, J. Cloning and promoter identification of the iron-regulated cir gene of Escherichia coli. J. Bacteriol. 169, 5343–5352 (1987).

    Article  CAS  Google Scholar 

  4. Nogueira, R.A. & Varanda, W.A. Gating properties of channels formed by colicin Ia in planar lipid bilayer membranes. J. Membrane Biol. 105, 143–153 (1988).

    Article  CAS  Google Scholar 

  5. Tokuda, H. & Konisky, J. Mode of action of colicin Ia: Effect of colicin on the Escherichia coli proton electrochemical gradient. Proc. natn. Acad. Sci. U.S.A. 75, 2579–2583 (1978).

    Article  CAS  Google Scholar 

  6. Tokuda, H. & Konisky, J. Effects of colicins Ia and E1 on permeability of liposomes. Proc. natn. Acad. Sci. U.S.A. 76, 6167–6171 (1979).

    Article  CAS  Google Scholar 

  7. Cramer, W.A., Cohen, F.S., Merrill, A.R. & Song, H.Y. Structure and dynamics of the colicin E1 channel. Molec. Microbiol. 4, 519–526 (1990).

    Article  CAS  Google Scholar 

  8. Pattus, F. et al. Colicins: Prokaryotic killer-pores. Experientia 46, 180–192 (1990).

    CAS  Google Scholar 

  9. Donovan, J.J., Simon, M.I., Draper, R. & Montal, M. Diphtheria toxin forms transmembrane channels in planar lipid bilayers. Proc. natn. Acad. Sci. U.S.A. 78, 172–176 (1981).

    Article  CAS  Google Scholar 

  10. Holmgren, J. Actions of cholera toxin and the prevention and treatment of cholera. Nature 292, 413–417 (1981).

    Article  CAS  Google Scholar 

  11. Young, J.D.-E., Cohn, Z.A. & Podack, E.R. The ninth component of complement and the pore-forming protein (perforin 1) from cytotoxic T cells: Structural, immunological, and functional similarities. Science 233, 184–190 (1986).

    Article  CAS  Google Scholar 

  12. Wilson, A.J.C. The probability distribution of X-ray intensities. Acta crystallogr. 2, 318–321 (1949).

    Article  Google Scholar 

  13. Wang, B.C. Resolution of phase ambiguity in macromolecular crystallography. Meth. Enzymol. 115, 90–112 (1985).

    Article  CAS  Google Scholar 

  14. Choe, S., Konisky, J. & Stroud, R.M. Structure of a channel-forming colicin Ia. Biophys. J. 51, 249a (1987).

    Article  Google Scholar 

  15. Mel, S.F. & Stroud, R.M. Colicin Ia inserts into negatively charged membranes at low pH with a tertiary but little secondary structural change. Biochemistry 32, 2082–2089 (1993).

    Article  CAS  Google Scholar 

  16. Jones, T.A. & Thirrup, S. Using know substructures in protein model building and crystallography. EMBO J. 5, 819–822 (1986).

    Article  CAS  Google Scholar 

  17. Konisky, J. & Richards, F.M. Characterization of colicin Ia and colicin Ib: Purification and some physical properties. J. biol. Chem. 245, 2972–2978 (1970).

    CAS  PubMed  Google Scholar 

  18. Schwartz, S.A. & Helinski, D.R. Purification and characterization of colicin E1. J. biol. Chem. 246, 6318–6327 (1971).

    CAS  PubMed  Google Scholar 

  19. Benedetti, H., Lloubès, R., Lazdunski, C. & Letellier, L. Colicin A unfolds during its translocation in Escherichia coli cells and spans the whole cell envelope when its pore has formed. EMBO J. 11, 441–447 (1992).

    Article  CAS  Google Scholar 

  20. Ohno-Iwashita, Y. & Imahori, K. Assignment of the functional loci in the colicin E1 molecule by characterization of its proteolytic fragments. J. biol. Chem. 257, 6446–6451 (1982).

    CAS  PubMed  Google Scholar 

  21. Carmen Martinez, M., Lazdunski, C. & Pattus, F. Isolation, molecular and functional properties of the C-terminal domain of colicin A. EMBO J. 2, 1501–1507 (1983).

    Article  Google Scholar 

  22. Baty, D. et al. Functional domains of colicin A. Molec. Microbiol. 2, 807–811 (1988).

    Article  CAS  Google Scholar 

  23. Baty, D., Lakey, J., Pattus, F. & Lazdunski, C. A 136-amino-acid-residue COOH-terminal fragment of colicin A is endowed with ionophoric activity. Eur. J. Biochem. 189, 409–413 (1990).

    Article  CAS  Google Scholar 

  24. Cleveland, M.v., Slatin, S., Finkelstein, A. & Levinthal, C. Structure-function relationships for a voltage-dependent ion channel: Properties of COOH-terminal fragments of colicin E1. Proc. natn. Acad. Sci. U.S.A. 80, 3706–3710 (1983).

    Article  CAS  Google Scholar 

  25. Ghosh, P., Mel, S.F. & Stroud, R.M. A carboxy-terminal fragment of colicin Ia forms ion channels. J. Membrane Biol. 134, 85–92 (1993).

    Article  CAS  Google Scholar 

  26. Parker, M.W., Pattus, F., Tucker, A.D. & Tsernoglou, D. Structure of the membrane-pore-forming fragment of colicin A. Nature 337, 93–96 (1989).

    Article  CAS  Google Scholar 

  27. Parker, M.W.M., Postma, J.P., Pattus, F., Tucker, A.D. & Tsernoglou, D. Refined structure of the pore-forming domain of colicin A at 2.4 Å resolution. J. molec. Biol. 224, 639–657 (1992).

    Article  CAS  Google Scholar 

  28. Wormald, M.R., Merrill, A.R., Cramer, W.A. & Williams, R.J.P. Solution NMR studies of colicin E1 C-terminal thermolytic peptide: Structural comparison with colicin A and the effects of pH changes. Eur. J. Biochem. 191, 155–161 (1990).

    Article  CAS  Google Scholar 

  29. Shin, Y.-K., Levinthal, C., Levinthal, F. & Hubbell, W.L. Colicin E1 binding to membranes: Time-resolved studies of spin-labeled mutants. Science 259, 960–963 (1993).

    Article  CAS  Google Scholar 

  30. Merrill, A.R. & Cramer, W.A. Identification of a voltage-responsive segment of the potential-gated colicin E1 ion channel. Biochemistry 29, 8529–8534 (1990).

    Article  CAS  Google Scholar 

  31. Mel, S.F., Falick, A.M., Burlingame, A.L. & Stroud, R.M. Mapping a membrane-associated conformation of colicin Ia. Biochemistry 32, 9473–9479 (1993).

    Article  CAS  Google Scholar 

  32. Benedetti, H., Lazdunski, C. & Lloubès, R. Protein Import into Escherichia coli: Colicins A and E1 Interact with a Component of their Translocation System. EMBO J. 10, 1989–1995 (1991).

    Article  CAS  Google Scholar 

  33. Frenette, M. et al. Interaction of colicin A domains with phospholipid monolayers and liposomes: Relevance to the mechanism of action. Biochemistry 28, 2509–2514 (1989).

    Article  CAS  Google Scholar 

  34. Lupas, A., Van Dyke, M. & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162–1164 (1991).

    Article  CAS  Google Scholar 

  35. Mankovich, J.A., Hsu, C. & Konisky, J. DNA and amino acid sequence analysis of structural and immunity genes of colicins Ia and Ib. J. Bacteriol. 168, 228–236 (1986).

    Article  CAS  Google Scholar 

  36. Ghosh, P. The structure and function of colicin Ia. Thesis, University of California, San Francisco (1992).

    Google Scholar 

  37. Maniatis, T., Fritsch, E.F. & Sambrook, J. Molecular Cloning (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1982).

    Google Scholar 

  38. Richardson, H., Emslie-Smith, A.H. & Senior, B.W. Agar diffusion method for the assay of colicins. Appl. Microbiol. 16, 1468–1474 (1968).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Terwilliger, T.C., Kim, S.-H. & Eisenberg, D. Generalized method of determining heavy-atom positions using the difference Patterson function. Acta crystallogr. A43, 1–5 (1987).

    Article  CAS  Google Scholar 

  40. Terwilliger, T.C., Kim, S.-H. & Eisenberg, D. Isomorphous relacement: Effects of errors on the phase probability distribution. Acta crystallogr. A43, 6–13 (1987).

    Article  CAS  Google Scholar 

  41. Vaughan, P.A., Sturdivant, J.H. & Pauling, L. The determination of the structure of complex molecules and ions from X-ray diffraction by their solutions: The structures of the groups PtBr6−, PtCl6−, Nb6Cl12++, Ta6Br12++, and Ta6Cl12++. J. Am. chem. Soc. 72, 5477–5486 (1950).

    Article  CAS  Google Scholar 

  42. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta crystallogr. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  43. Carson, M. Ribbons 2.0. J. appl. Crystallogr. 24, 958–961 (1991).

    Article  Google Scholar 

  44. Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. The MIDAS display system. J. molec. Graphics 6, 13–27 (1988).

    Article  CAS  Google Scholar 

  45. Huang, C.C., Pettersen, E.F., Klein, T.E., Ferrin, T.E. & Langridge, R. Conic: A fast renderer for space-filling molecules with shadows. J. molec. Graphics 9, 230–236 (1991).

    Article  CAS  Google Scholar 

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Author information

Author notes

  1. Partho Ghosh

    Present address: Department of Biochemistry and Molecular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138

  2. Stephanie F. Mel

    Present address: Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115

Authors and Affiliations

  1. Departments of Biochemistry and Biophysics, University of California, San Francisco, California, 94143-0448, USA

    Robert M. Stroud

  2. Department of Experimental Pathology, University of California, San Francisco, California, 94143-0448, USA

    Stephanie F. Mel

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  1. Partho Ghosh
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  2. Stephanie F. Mel
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  3. Robert M. Stroud
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Ghosh, P., Mel, S. & Stroud, R. The domain structure of the ion channel-forming protein colicin Ia. Nat Struct Mol Biol 1, 597–604 (1994). https://doi.org/10.1038/nsb0994-597

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