Crystal structure at 1.2 Å resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase

EMBO Journal

Volumn 16, Issue 15, 1997, Pages 4760-4769

  Schmitt, Emmanuelle ^a   Mechulam, Yves ^a   Fromant, Michel ^a   Plateau, Pierre ^a   Blanquet, Sylvain ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

Crystalline structure; Esterase; Peptidyl tRNA; Translation

Indexed keywords

AMINOPEPTIDASE; HYDROLASE; TRANSFER RNA;

AEROMONAS; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; RNA TRANSLATION; SITE DIRECTED MUTAGENESIS;

AEROMONAS; AMINO ACID SEQUENCE; BINDING SITES; CARBOXYLIC ESTER HYDROLASES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; GENES, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; SUBSTRATE SPECIFICITY;

AEROMONAS; ESCHERICHIA COLI; VIBRIO PROTEOLYTICUS;

EID: 0030738859     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.15.4760     Document Type: Article

References (51)

1. Atherly, A.G. (1978) Peptidyl-transfer RNA hydrolase prevents inhibition of protein synthesis initiation. Nature, 275, 769.
2. Atherly, A.G. and Menninger, J.R. (1972) Mutant E.coli strain with temperature sensitive peptidyl-transfer RNA hydrolase. Nature New Biol., 240, 245-246.
3. Bacon, D.J. and Anderson, W.F. (1988) A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph., 6, 219-220.
4. Brevet, A., Chen, J., Lévêque, E. Blanquet, S. and Plateau, P. (1995) Comparison of the enzymatic properties of the two Escherichia coli lysyl-tRNA synthetase species. J. Biol. Chem., 270, 14439-14444.
5. Brünger, A.T. (1992a) X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
6. Brünger, A.T. (1992b) Free-R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-474.
7. Brunger, A.T., Kuryian, J. and Karplus, M. (1987) Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
8. Chapeville, F., Yot, P. and Paulin, D. (1969) Enzymatic hydrolysis of N-acylaminoacyl transfer RNAs. Cold Spring Harbor Symp. Quant. Biol., 34, 493-498.
9. Chevrier, B. (1994) PATGEN: an automatic program to generate theoretical Patterson peaks and to compare them with experimental Patterson peaks. J. Appl. Crystallogr., 27, 860-861.
10. Chevrier, B., Schalk, C., D'Orchymont, H., Rondeau, J.M. Moras, D. and Tarnus, C. (1994) Crystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family. Structure, 2, 283-291.
11. Collaborative Computational Project No. 4 (1994) The CCP4 suite: programs from protein crystallography. Acta Crystallogr., D50, 760-763.
12. Lys. J. Mol. Biol., 253, 100-113.
13. Cowtan, K. (1994) dm: an automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 34-38.
14. Csonka, L.N. and Clark, A.J. (1980) Construction of an Hfr strain useful for transferring recA mutations between Escherichia coli strains. J. Bacteriol., 143, 529-530.
15. Cuzin, F., Kretchmer, N., Greenberg, R.E., Hurwitz, R. and Chapeville, F. (1967) Enzymatic hydrolysis of N-substituted aminoacyl-tRNA. Proc. Natl Acad. Sci. USA, 58, 2079-2086.
16. Dardel, F. (1994) MC-Fit: Using Monte-Carlo methods to get accurate confidence limits on enzyme parameters. CABIOS, 10, 273-275.
17. Dutka, S., Meinnel, T., Lazennec, C. Mechulam, Y. and Blanquet, S. (1993) Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase. Nucleic Acids Res., 21, 4025-4030.
18. Fourmy, D., Meinnel, T., Mechulam, Y. and Blanquet, S. (1993) Mapping of the zinc binding domain of Escherichia coli methionyl-tRNA synthetase. J. Mol. Biol., 231, 1068-1077.
19. Garcia-Villegas, M.R., De La Vega, F.M., Galindo, J.M., Segura, M., Buckingham, R.H. and Guarneros, G. (1991) Peptidyl-tRNA hydrolase is involved in λ inhibition of host protein synthesis. EMBO J., 10, 3549-3555.
20. Gross, M., Crow, P. and White, J. (1992a) The site of hydrolysis by rabbit reticulocyte peptidyl-tRNA hydrolase is the 3′-AMP terminus of susceptible tRNA substrates. J. Biol. Chem., 267, 2080-2086.
21. Gross, M., Starn, T.K., Rundquist, C., Crow, P. White, J., Olm, A. and Wagner, T. (1992b) Purification and initial characterization of peptidyl-tRNA hydrolase from rabbit reticulocytes. J. Biol. Chem., 267, 2073-2079.
22. Metf formyltransferase. J. Mol. Biol., 224, 359-367.
23. Hamilton, C.M., Aldea, M., Washburn, B.K., Babitzke, P. and Kushner, S.R. (1989) New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol., 171, 4617-4622.
24. Henderson, D. and Weil, J. (1976) A mutant of Escherichia coli that prevents growth of phage lambda and is bypassed by lambda mutants in a nonessential region of the genome. Virology, 71, 546-559.
25. Lys. EMBO J., 15, 2826-2833.
26. Higgins, D.G. and Sharp, P.M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS, 5, 151-153.
27. Hirel, P.-H., Lévêque, F., Mellot, F., Dardel, F., Panvert, M., Mechulam, Y. and Fayat, G. (1988) Genetic engineering of methionyl-tRNA synthetase: in vitro regeneration of an active synthetase by proteolytic cleavage of a methionyl-tRNA synthetase-β-galactosidase chimeric protein. Biochimie, 70, 773-782.
28. Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Cystallogr., A47, 110-119.
29. Jost, J.P. and Bock, R.M. (1969) Enzymatic hydrolysis of N-substituted aminoacyl transfer ribonucleic acid in yeast. J. Biol. Chem., 244, 5866-5873.
30. Kabsch, W.J. (1988) Evaluation of single crystal X-ray diffraction data from a position sensitive detector. J. Appl. Crystallogr., 21, 916-924.
31. Kleijwegt, G.J. and Jones, T.A. (1994) Proceedings of the CCP4 Study Weekend: From First Map to Final Model. SERC Daresbury Laboratory, Warrington, UK, pp. 59-66.
32. Koellner, G., Luic, M., Shugar, D., Saenger, W. and Bzowska, A. (1997) Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 Å resolution. J. Mol. Biol., 265, 202-216.
33. Kössel, H. (1969) Purification and properties of peptidyl-tRNA hydrolase from Escherichia coli. Biochim. Biophys. Acta, 204, 191-202.
34. Kössel, H. and RajBhandary, U.L. (1968) Studies on polynucleotides. LXXXVI. Enzymic hydrolysis of N-acylaminoacyl-transfer RNA. J. Mol. Biol., 35, 539-560.
35. Kraulis, P. (1991) A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
36. Laskowski, R.A., Mac Arthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr., 26, 283-291.
37. Lee, C.P., Seong, B.L. and RajBhandary, U.L. (1991) Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem. J. Biol. Chem., 266, 18012-18017.
38. Luzatti, P.V. (1952) Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallogr., 5, 802-810.
39. Mayaux, J.-F. and Blanquet, S. (1981) Binding of zinc to Escherichia coli phenylalanyl transfer ribonucleic acid synthetase. Comparison with other aminoacyl transfer ribonucleic acid synthetases. Biochemistry, 20, 4647-4654.
40. Menninger, J.R. (1976) Peptidyl-transfer RNA dissociates during protein synthesis from ribosomes of Escherichia coli. J. Biol. Chem., 251, 3392-3398.
41. Menninger, J.R. (1978) The accumulation as peptidyl-transfer RNA of isoaccepting transfer RNA families in E.coli with temperature-sensitive peptidyl-tRNA hydrolase. J. Biol. Chem., 253, 6808-6813.
42. Menninger, J.R. (1979) Accumulation of peptidyl-tRNA is lethal to Escherichia coli. J. Bacteriol., 137, 694-696.
43. Menninger, J.R. and Coleman, R.A. (1993) Lincosamide antibiotics stimulate dissociation of peptidyl-tRNA from ribosomes. Antimicrob. Agents Chemother., 37, 2027-2029.
44. Nicholls, A. and Honig, B. (1991) A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem., 12, 435-445.
45. Nicholls, A., Sharp, K.A. and Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-286.
46. Otwinowski, Z. (1991) Maximum likelihood refinement of heavy atom parameters. In Wolf, W., Evans, P.R. and Leslie, A.G.W. (eds), Isomorphous Replacement and Anomalous Scattering. Science and Engineering Research Council, Warrington, UK, pp. 80-86.
47. Sayers, J.R., Schmidt, W. and Eckstein, F. (1988) 5′-3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis. Nucleic Acids. Res., 16, 791-802.
48. Schmitt, E., Fromant, M., Plateau, P. Mechulam, Y. and Blanquet, S. (1997) Crystallization and preliminary X-ray analysis of Escherichia coli peptidyl-tRNA hydrolase. Proteins, 28, 135-136.
49. Schulman, L. and Pelka, H. (1975) The structural basis for the resistance of Escherichia coli formylmethionyl transfer ribonucleic acid to cleavage by Escherichia coli peptidyl transfer ribonucleic acid hydrolase. J. Biol. Chem., 250, 542-547.
50. Shiloach, J., Bauer, S., De Groot, N. and Lapidot, Y. (1975a) The influence of the peptide chain length on the activity of peptidyl-tRNA hydrolase from E.coli. Nucleic Acids Res., 2 1941-1950.
51. Shiloach, J., Lapidot, Y., de Groot, N., Sprinzl, M. and Cramer, F. (1975b) The specificity of peptidyl-tRNA hydrolase from E.coli. FEBS Lett., 57, 130-133.