Structural and mutational studies of the catalytic domain of colicin E5: A tRNA-specific ribonuclease

Biochemistry

Volumn 44, Issue 31, 2005, Pages 10494-10500

  Lin, Yi Lun ^a   Elias, Youssef ^a   Huang, Raven H ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CATALYST ACTIVITY; CELL CULTURE; CRYSTAL STRUCTURE; ESCHERICHIA COLI; MUTAGENESIS; PROTEINS; RNA; SYNTHESIS (CHEMICAL);

CATALYTIC DOMAINS; CELL DEATH; RNA BINDING;

ENZYMES;

COLICIN; COLICIN E5; HISTIDINE; NUCLEOTIDE; QUEUOSINE; RIBONUCLEASE; RIBONUCLEASE T1; TRANSFER RNA; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CELL DEATH; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN RNA BINDING; PROTEIN SYNTHESIS INHIBITION; RNA BINDING; RNA CLEAVAGE;

AMINO ACID SUBSTITUTION; BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; COLICINS; CRYSTALLOGRAPHY, X-RAY; DNA MUTATIONAL ANALYSIS; ESCHERICHIA COLI PROTEINS; HYDROLYSIS; PENTOSYLTRANSFERASES; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASES; RNA, BACTERIAL; RNA, TRANSFER; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI;

EID: 23244431996     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050749s     Document Type: Article

References (36)

1. Stillmark, H. (1888) in Inaugural Dissertation, Dorpat, Estonia.
2. Olson, B. H., and Goerner, G. L. (1965) Alpha Sarcin, a New Antitumor Agent. I. Isolation, Purification, Chemical Composition, and the Identity of a New Amino Acid, Appl. Microbiol. 13, 314-21.
3. Jennings, J. C., Olson, B. H., Roga, V., Junek, A. J., and Schuurmans, D. M. (1965) Alpha Sarcin, a New Antitumor Agent. II. Fermentation and Antitumor Spectrum, Appl. Microbiol. 13, 322-6.
4. James, R., Kleanthous, C., and Moore, G. R. (1996) The biology of E colicins: Paradigms and paradoxes, Microbiology 142 (Part 7), 1569-80.
5. Endo, Y., Mitsui, K., Motizuki, M., and Tsurugi, K. (1987) The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28S ribosomal RNA caused by the toxins, J. Biol. Chem. 262, 5908-12.
6. Endo, Y., and Tsurugi, K. (1987) RNA N-glycosidase activity of ricin A-chain. Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes, J. Biol. Chem. 262, 8128-30.
7. Endo, Y., and Wool, I. G. (1982) The site of action of α-sarcin on eukaryotic ribosomes. The sequence at the α-sarcin cleavage site in 28S ribosomal ribonucleic acid, J. Biol. Chem. 257, 9054-60.
8. Bowman, C. M., Dahlberg, J. E., Ikemura, T., Konisky, J., and Nomura, M. (1971) Specific inactivation of 16S ribosomal RNA induced by colicin E3 in vivo, Proc. Natl. Acad. Sci. U.S.A. 68, 964-8.
9. Senior, B. W., and Holland, I. B. (1971) Effect of colicin E3 upon the 30S ribosomal subunit of Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 68, 959-63.
10. Masaki, H., and Ogawa, T. (2002) The modes of action of colicins E5 and D, and related cytotoxic tRNases, Biochimie 84, 433-8.
11. Depew, R. E., and Cozzarelli, N. R. (1974) Genetics and physiology of bacteriophage T4 3′-phosphatase: Evidence for involvement of the enzyme in T4 DNA metabolism, J. Virol. 13, 888-97.
12. Kaufmann, G. (2000) Anticodon nucleases, Trends Biochem. Sci. 25, 70-4.
13. Tomita, K., Ogawa, T., Uozumi, T., Watanabe, K., and Masaki, H. (2000) A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops, Proc. Natl. Acad. Sci. U.S.A. 97, 8278-83.
14. Ogawa, T., Tomita, K., Ueda, T., Watanabe, K., Uozumi, T., and Masaki, H. (1999) A cytotoxic ribonuclease targeting specific transfer RNA anticodons, Science 283, 2097-100.
15. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, in Methods in Enzymology, pp 307-26, Academic Press, San Diego.
16. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr. D55 (Part 4), 849-61.
17. Terwilliger, T. C. (1999) Reciprocal-space solvent flattening, Acta Crystallogr. D55, 1863-71.
18. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A47, 110-9.
19. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination, Acta Crystallogr. D54, 905-21.
20. Shi, H., and Moore, P. B. (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6, 1091-105.
21. DeLano, W. L. (2002) The PyMOL Molecular Graphic System, DeLano Scientific, South San Francisco, CA.
22. Carr, S., Walker, D., James, R., Kleanthous, C., and Hemmings, A. M. (2000) Inhibition of a ribosome-inactivating ribonuclease: The crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein, Struct. Folding Des. 8, 949-60.
23. Soelaiman, S., Jakes, K., Wu, N., Li, C., and Shoham, M. (2001) Crystal structure of colicin E3: Implications for cell entry and ribosome inactivation, Mol. Cell 8, 1053-62.
24. Ko, T. P., Liao, C. C., Ku, W. Y., Chak, K. F., and Yuan, H. S. (1999) The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein, Struct. Folding Des. 7, 91-102.
25. Hsia, K. C., Chak, K. F., Liang, P. H., Cheng, Y. S., Ku, W. Y., and Yuan, H. S. (2004) DNA binding and degradation by the HNH protein Co1E7, Structure 12, 205-14.
26. Kleanthous, C., Kuhlmann, U. C., Pommer, A. J., Ferguson, N., Radford, S. E., Moore, G. R., James, R., and Hemmings, A. M. (1999) Structural and mechanistic basis of immunity toward endonuclease colicins, Nat. Struct. Biol. 6, 243-52.
27. Holm, L., and Sander, C. (1993) Protein structure comparison by alignment of distance matrices, J. Mol. Biol. 233, 123-38.
28. Takagi, H., Kakuta, Y., Okada, T., Yao, M., Tanaka, I., and Kimura, M. (2005) Crystal structure of archaeal toxin-antitoxin ReIE-ReIB complex with implications for toxin activity and antitoxin effects, Nat. Struct. Mol. Biol. (in press).
29. Graille, M., Mora, L., Buckingham, R. H., Van Tilbeurgh, H., and De Zamaroczy, M. (2004) Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein, EMBO J. 23, 1474-82.
30. Martinez-Oyanedel, J., Choe, H. W., Heinemann, U., and Saenger, W. (1991) Ribonuclease T1 with free recognition and catalytic site: Crystal structure analysis at 1.5 Å resolution, J. Mol. Biol. 222, 335-52.
31. Steyaert, J. (1997) A decade of protein engineering on ribonuclease T1 : Atomic dissection of the enzyme-substrate interactions, Eur. J. Biochem. 247, 1-11.
32. Hoang, C., and Ferre-D'Amare, A. R. (2001) Cocrystal structure of a tRNA ψ55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme, Cell 107, 929-39.
33. Xie, W., Liu, X., and Huang, R. H. (2003) Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate, Nat. Struct. Biol. 10, 781-8.
34. Yang, X., Gerczei, T., Glover, L. T., and Correll, C. C. (2001) Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping, Nat. Struct. Biol. 8, 968-73.
35. Schreiber, G., Frisch, C., and Fersht, A. R. (1997) The role of Glu73 of barnase in catalysis and the binding of barstar, J. Mol. Biol. 270, 111-22.
36. Thompson, J. E., and Raines, R. T. (1994) Value of general acid-base catalysis to ribonuclease A, J. Am. Chem. Soc. 116, 5467-8.