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The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p

Nature Structural Biology volume 5, pages 140–147 (1998)Cite this article

Abstract

The structure of the two N-terminal domains of the gene 3 protein of filamentous phages (residues 1–217) has been solved by multiwavelength anomalous diffraction and refined at 1.46 A resolution. Each domain consists of either five or eight β-strands and a single α-helix. Despite missing sequence homology, their cores superimposed with a root-mean-square deviation of 2 ?. The domains are engaged in extensive interactions, resulting in a horseshoe shape with aliphatic amino acids and threonines lining the inside, delineating the likely binding site for the F-pilus. The glycine-rich linker connecting the domains is invisible in the otherwise highly ordered structure and may confer flexibility between the domains required during the infection process.

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References

  1. Smith, G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 (1985).

    Article  CAS  Google Scholar 

  2. Phizicky, E.M. & Fields, S. Protein–protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94–123 (1995).

    CAS  PubMed Central  Google Scholar 

  3. Cortese, R. et al Selection of biologically active peptides by phage display of random peptide libraries. Curr. Opin. Biotechnol. 7, 616–621 (1996).

    Article  CAS  Google Scholar 

  4. Dunn, I.S. Phage display of proteins. Curr. Opin. Biotechnol. 7, 547–553 (1996).

    Article  CAS  Google Scholar 

  5. Spada, S., Krebber, C. & Plückthun, A. Selectively infective phages (SIP). Biol. Chem. 378, 445–456 (1997).

    CAS  Google Scholar 

  6. Gray, C.W., Brown, R.S. & Marvin, D.A. Adsorption complex of filamentous fd virus. J. Mol. Biol. 146, 621–627 (1981).

    Article  CAS  Google Scholar 

  7. Jacobson, A. Role of F pili in the penetration of bacteriophage fl. J. Virol. 10, 835–843 (1972).

    CAS  PubMed Central  Google Scholar 

  8. Sun, T.P. & Webster, R.E. fii, a bacterial locus required for filamentous phage infection and its relation to colicin-tolerant tolA and tolB. J. Bacterial. 165, 107–115 (1986).

    Article  CAS  Google Scholar 

  9. Sun, T.P. & Webster, R.E. Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli. J. Bacteriol. 169, 2667–2674 (1987).

    Article  CAS  Google Scholar 

  10. Riechmann, L. & Holliger, P. The C-terminal domain of TolA is the coreceptorfor filamentous phage infection of E. coli. Cell 90, 351–360 (1997).

    Article  CAS  Google Scholar 

  11. Nelson, F.K., Friedman, S.M. & Smith, G.P. Filamentous phage DNA cloning vectors: a noninfective mutant with a nonpolar deletion in gene III. Virology 108, 338–350 (1981).

    Article  CAS  Google Scholar 

  12. Crissman, J.W. & Smith, G.P. Gene-Ill protein of filamentous phages: evidence for a carboxyl-terminal domain with a role in morphogenesis. Virology 132, 445–455 (1984).

    Article  CAS  Google Scholar 

  13. Endemann, H., Gailus, V. & Rasched, I. Interchangeability of the adsorption proteins of bacteriophages Ff and IKe. J. Virol. 67, 3332–3337 (1993).

    CAS  PubMed Central  Google Scholar 

  14. Hutchinson, E.G. & Thornton, J.M. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212–220 (1996).

    Article  CAS  Google Scholar 

  15. Holm, L. & Sander, C Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138 (1993).

    Article  CAS  Google Scholar 

  16. Cabral, J.H, et al. Crystal structure of a PDZ domain. Nature 382, 649–652 (1996).

    Article  CAS  Google Scholar 

  17. Faber, H.R. et al. 1.8 ? crystal structure of the C-terminal domain of rabbit serum haemopexin. Structure 3, 551–559 (1995).

    Article  CAS  Google Scholar 

  18. Viguera, A.R., Blanco, F.J. & Serrano, L. The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247, 670–681 (1995).

    CAS  Google Scholar 

  19. Holliger, P. & Riechmann, L. A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage Fd. Structure 5, 265–275 (1997).

    Article  CAS  Google Scholar 

  20. Koradi, R., Billeter, M. & Wüthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–5, 29–32 (1996).

    Article  CAS  Google Scholar 

  21. Baldwin, E.T. et al. Crystal structure of interleukin-8: symbiosis of NMR and crystallography. Proc. Natl. Acad. Sci. USA 88, 502–506 (1991).

    Article  CAS  Google Scholar 

  22. Lubkowski, J. et al. The structure of MCP-1 in two crystal forms provides a rare example of variable quarternary interactions. Nature Struct. Biol. 4, 64–69 (1997).

    Article  CAS  Google Scholar 

  23. Stengele, I., Bross, P., Garces, X., Giray, J. & Rasched, I. Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites. J. Mol. Biol. 212, 143–149 (1990).

    Article  CAS  Google Scholar 

  24. Krebber, C. et al. Selectively-infective phage (SIP): a mechanistic dissection of a novel in vivo selection for protein-ligand interactions. J. Mol. Biol. 268, 607–618 (1997).

    Article  CAS  Google Scholar 

  25. Peters, B.P.H., Peters, R.M., Schoenmakers, J.G.G. & Konings, R.N.H. Nucleotide sequence and genetic organizaton of the genome of the N-specific filamentous bacteriophage IKe. Comparison with the genome of the F-specific filamentous phages M13, fd and fl. J. Mol. Biol. 181, 27–39 (1985).

    Article  Google Scholar 

  26. Frost, L.S., Ippen-lhler, K. & Skurray, R.A. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev. 58, 162–210 (1994).

    CAS  PubMed Central  Google Scholar 

  27. Marvin, D.A. & Folkhard, W. Structure of F-pili: reassessment of the symmetry. J. Mol. Biol. 191, 299–300 (1986).

    Article  CAS  Google Scholar 

  28. Glucksman, M.J., Bhattacharjee, S. & Makowski, L. Three-dimensional structure of a cloning vector. X-ray diffraction studies of filamentous bacteriophage M13 at 7? resolution. J. Mol. Biol. 226, 455–470 (1992).

    Article  CAS  Google Scholar 

  29. Lin, T.C., Webster, R.E. & Konigsberg, W. Isolation and characterization of the C and D proteins coded by gene IX and gene VI in the filamentous bacteriophage fl and fd. J. Biol. Chem. 255, 10331–10337 (1980).

    CAS  Google Scholar 

  30. Grant, R.A., Lin, T.C., Webster, R.E. & Konigsberg, W. Structure of filamentous bacteriophage: isolation, characterization, and localization of the minor coat proteins and orientation of the DNA. Prog. Clin. Biol. Res. 64: 413–428 (1981).

    CAS  Google Scholar 

  31. Tzagoloff, H. & Pratt, D. The initial steps in infection with coliphage M13. Virology 24, 372–380 (1964).

    Article  CAS  Google Scholar 

  32. Goldsmith, M.E. & Konigsberg, W.H. Adsorption protein of the bacteriophage fd: isolation, molecular properties, and location in the virus. Biochemistry 16, 2686–2694 (1977).

    Article  CAS  Google Scholar 

  33. Beck, E. & Zink, B. Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd. Gene 16, 35–58 (1981).

    Article  CAS  Google Scholar 

  34. Freund, C., Ross, A., Guth, B., Plückthun, A. & Holak, T.A. Characterization of the linker peptide of the single-chain Fv fragment of an antibody by NMR spectroscopy. FEBS Lett. 320, 97–100 (1993).

    Article  CAS  Google Scholar 

  35. S tudier, F.W. & Moffatt, B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189, 113–130 (1986).

    Article  Google Scholar 

  36. Qoronfleh, M.W. et al. Production of selenomethionine-labeled recombinant human neutrophil collagenase in Escherichia coli. J. Biotechnol. 39, 119–128 (1995).

    Article  CAS  Google Scholar 

  37. Plückthun, A., et al. Producing antibodies in Escherichia coli: from PCR to fermentation. In Antibody engineering: a practical approach (eds McCafferty, J. & Hoogenboom, H.R., Chriswell, D.J.) 203–252 (IRL Press, Oxford; 1996).

    Google Scholar 

  38. Hendrickson, W.A., Horton, J.R. & LeMaster, D.M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three dimensional structure. EMBO J. 9, 1665–1672 (1990).

    Article  CAS  Google Scholar 

  39. Matthews, B.W. Solvent content of protein crystals. J. Mol. Biol. 33, 491–497 (1968).

    Article  CAS  Google Scholar 

  40. Otwinowski, Z. An oscillation data processing suite for macromolecular crystallography (Yale University, New Haven, Connecticut, USA; 1992).

  41. Jones, T.A. & Kjeldgaard, M.O — the manual (Uppsala University, Uppsala, 1994).

  42. Brünger, A. X-plor version 3.1: a system for X-ray crystallography and NMR (Yale University Press, New Haven, Connecticut, USA; 1992).

    Google Scholar 

  43. Furey, W. & Swaminathan, S. PHASES - A program package for the processing and analysis of diffraction data for macromolecules. Acta Crystallogr. 18, 73 (1990).

    Google Scholar 

  44. Sheldrick, G.M. Patterson superposition and ab initio phasing. Meth. Enz. 276, 628–641 (1997).

    Article  CAS  Google Scholar 

  45. Wang, B.C. Resolution of phase ambiguity in macromolecular crystallography. Meth. Enz. 115, 90- 112 (1985).

    Article  CAS  Google Scholar 

  46. CCP4:SERC Collaborative computing project no.4 (Warrington, UK; 1979).

  47. Lundblad, R.L. & Noyes, C.M. Chemical modification of tryptophan. In Chemical reagents for protein modification (eds. Lundblad, R.L. & Noyes, C.M.) 47–71 (CRC Press, Boca Raton, Florida; 1984 ).

    Google Scholar 

  48. 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 

  49. Carson, M. RIBBONS 4.0. J. Appl.Crystallogr. 24, 958–961 (1991).

    Article  Google Scholar 

  50. 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, 283–291 (1993).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Macromolecular Structure Laboratory, ABL-Basic Research Program, NCI-FCRDC, P.O. Box B, Frederick, Maryland, 21702, USA

    Jacek Lubkowski & Alexander Wlodawer

  2. Biochemisches Institut, Universität Zürich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland

    Frank Hennecke & Andreas Plückthun

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  1. Jacek Lubkowski
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  2. Frank Hennecke
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Correspondence to Alexander Wlodawer.

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Lubkowski, J., Hennecke, F., Plückthun, A. et al. The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p. Nat Struct Mol Biol 5, 140–147 (1998). https://doi.org/10.1038/nsb0298-140

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