Crystal structure of colicin E3 immunity protein: An inhibitor of a ribosome-inactivating RNase

Structure

Volumn 7, Issue 11, 1999, Pages 1365-1372

  Chunmin, Li ^a,c   Zhao, Dong ^a,c   Djebli, Abdellah ^b   Shoham, Menachem ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Bacteriocin; Colicin; Crystal structure; RNase inhibitor; Toxin

Indexed keywords

BACTERIOCIN; COLICIN; COLICIN E3; DNA TOPOISOMERASE; NUCLEIC ACID BINDING PROTEIN; RIBONUCLEASE; RIBOSOME INACTIVATING PROTEIN; RNA 16S; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME INHIBITION; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS;

ESCHERICHIA COLI;

EID: 0033571103     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)80026-X     Document Type: Article

References (46)

1. Jakes, K.S. (1982). The mechanism of action of colicin E2, colicin E3 and cloacin DF13. In Molecular Action of Toxins and Viruses. (Cohen, P. & van Heyningen, S., eds), pp. 131-167, Elsevier Biomedical Press, Amsterdam.
2. Walker, G.C. (1984). Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev. 48, 60-93.
3. De Graaf, F.K. & Oudega, B. (1986). Production and release of cloacin DF13 and related colicins. Curr. Top. Microbiol. Immunol. 125, 183-205.
4. 12 and E colicins on the outer membrane of the cell envelope. J. Bacteriol. 115, 506-513.
5. James, R., Kleanthous, C. & Moore, G.R. (1996). The biology of E colicins: Paradigms and paradoxes. Microbiology 142, 1569-1580.
6. 12 receptor with high affinity for colicin E3. J. Biol. Chem. 273, 31113-31118.
7. 12 resulting from insertion mutations in the Escherichia coli btuB gene. J. Biol. Chem. 263, 14224-14230.
8. Bouveret, E., Rigal, A., Lazdunski, C. & Benedetti, H. (1997). The N-terminal domain of colicin E3 interacts with TolB which is involved in the colicin translocation step. Mol. Microbiol. 23, 909-920.
9. Nomura, M. (1967). Colicins and related bacteriocins. Annu. Rev. Microbiol. 21, 257-284.
10. Nomura, M., Sidikaro, J., Jakes, K. & Zinder, N. (1974). In Ribosomes (M. Nomura, A. Tissieres & P. Lengyel, eds), pp.805-814, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
11. Konisky, J. & Nomura, M. (1967). Interactions of colicins with bacterial cells. II. Specific alteration of Escherichia coli ribosomes induced by colicin E3 in vivo. J. Mol. Biol. 26, 181-195.
12. Bowman, C.M., Dahlberg, J.E., Ikemura, T., Konisky, J. & Nomura, M. (1971). Specific inactivation of 16S ribosomal RNA by colicin E3 in vivo. Proc. Natl Acad. Sci. USA 68, 964-968.
13. Senior, B.W. & Holland, I.B. (1971 ). Effect of colicin E3 upon the 30S ribosomal subunit of Escherichia coli. Proc. Natl Acad. Sci. USA 68, 959-963.
14. Lasater, L.S., Cann, P.A. & Glitz, D.G. (1989). Localization of the site of cleavage of ribosomal RNA by colicin E3. Placement on the small ribosomal subunit by electron microscopy of antibody-complementary oligodeoxynucleotide complexes. J. Biol. Chem. 264, 21798-21805.
15. Boon, T. (1971). Inactivation of ribosomes in vitro by colicin E3. Proc. Natl Acad. Sci. USA 68, 2421-2425.
16. Bowman, C.M., Sidikaro, J. & Nomura, M. (1971). Specific inactivation of ribosomes by colicin E3 in vitro and mechanism of immunity in colicinogenic cells. Nat. New Biol. 234, 133-137.
17. De Graaf, F.K. & Klaasen-Boor, P. (1974). Purification and characterization of cloacin DF13 immunity protein. FEBS Lett. 40, 293-296.
18. Jakes, K., Zinder, N.D. & Boon, T. (1974). Purification and properties of colicin E3 immunity protein. J. Biol. Chem. 249,438-444.
19. Sidikaro, J. & Nomura, M. (1974). E3 immunity substance. A protein from e3-colicinogenic cells that accounts for their immunity to colicin E3. J. Biol. Chem. 245, 445-453.
20. Jakes, K. & Zinder, N.D. (1974). Highly purified colicin E3 contains immunity protein. Proc. Natl Acad. Sci. USA 71, 3380-3384.
21. Masaki, H., Akutsu, A., Uozumi, T. & Ohta, T. (1991). Identification of a unique specificity determinant of the colicin E3 immunity protein. Gene 107, 133-138.
22. Masaki, H. & Ohta, T. (1985). Colicin E3 and its immunity genes. J. Mol. Biol. 182, 217-227.
23. Mock, M., Miyada, C.G. & Gunsalus, R.P. (1983). Nucleotide sequence for the catalytic domain of colicin E3 and its immunity protein. Evidence for a third gene overlapping colicin. Nucleic Acids Res. 11, 3547-3557.
24. Baker, E.N., et al., & Reynolds, C.D. (1988). The structure of 2Zn pig insulin crystals at 1.5 Å resolution. Phil. Trans. R. Soc. Lond. B 319, 369-456.
25. Yajima, S., et al., & Uozomi, T. (1993). The three-dimensional structure of the colicin E3 immunity protein by distance geometry calculation. FEBS Lett. 333, 257-260.
26. Shoham, M. & Djebli, A. (1992). Structural studies on colicin E3 and its immunity protein. In NATO ASI Series H65. Bacteriocins, Microcins and Lantibiotics. (James, R., Lazdunski, C. & Pattus, F., eds), pp. 203-214, Springer-Verlag, Heidelberg, Germany.
27. 15N two-dimensional NMR spectroscopy. Biochemistry 31, 5578-5586.
28. Wallis, R., et al., & Kleanthous, C. (1995). Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 2. Cognate and noncognate interactions that span the millimolar to femtomolar affinity range. Biochemistry 34, 13751-13759.
29. Chak, K.F., Safo, M.K., Ku, W.Y., Hsieh, S.Y. & Yuan, H.S. (1996). The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface. Proc. Natl Acad. Sci. USA 93, 6437-6442.
30. 13C nuclear magnetic resonance assignments of the colicin E9 immunity protein Im9. Biochemistry 35, 9505-9512.
31. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
32. Lima, C.D., Wang, J.C. & Mondragon, A. (1994). Three-dimensional structure of the 67K N-terminal fragment of E. Coli DNA topoisomerase I. Nature 367, 138-146.
33. Nagai, K., Oubridge, C., Jessen, T.H., Li, J. & Evans, P.R. (1990). Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature 348, 515-520.
34. Oubridge, C., Ito, N., Evans, P.R., Teo, C.H. & Nagai, K. (1994). Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372, 432-438.
35. Perisic O., Fong, S., Lynch, D.E., Bycroft, M. & Williams, R.L. (1998). Crystal structure of a calcium-phospholipid binding domain from cytosolic phospholipase A2. J. Biol. Chem. 273, 1596-1604.
36. Levinson, B.L., Pickover, C.A. & Richards, F.M. (1983). Dimerization of colicin E3 in the absence of immunity protein. J. Biol. Chem. 258, 10967-10972.
37. Hershman, H.R. & Helinski, D.R. (1967). Purification and characterization of colicin E2 and colicin E3. J. Biol. Chem. 242, 5360-5368.
38. Collaborative Computational Project, Number 4. (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-776.
39. Otwinowski, Z. (1991). Maximum likelihood refinement of heavy-atom parameters in isomorphous replacement and anomalous scattering. In Proceedings of The CCP4 Study Weekend. (Wolf, W., Evans, P.R. & Leslie, A.G.E., eds), pp. 80-86, SERC Daresbury Laboratory, Warrington, UK.
40. Cowtan, K. (1994). DM: An automated procedure for phase improvement by density modification. In Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography. No. 31, pp. 34-48, SERC Daresbury Laboratory, Warrington, UK.
41. Jones, T.A., Zou, J-Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
42. Brünger, A.T., et al., & Warren, G.L. (1998). Crystallography and NMR system: A new software system for macromolecular structure determination. Acta Crystallogr. D 54, 905-921.
43. Kraulis, P.J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
44. Merritt, E.A. & Murphy, M.E. (1994). Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869-873.
45. Nicholls, A., Sharp, K. & Honig, B. (1991 ). Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
46. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.