Substrate recognition ability differs among various prokaryotic tRNase Zs

Biochemical and Biophysical Research Communications

Volumn 345, Issue 1, 2006, Pages 385-393

  Minagawa, Asako ^a   Takaku, Hiroaki ^a   Shibata, Hirotaka S ^a   Ishii, Ryohei ^b   Takagi, Masamichi ^a   Yokoyama, Shigeyuki ^b,c,d   Nashimoto, Masayuki ^a  

^a NIIGATA UNIVERSITY OF PHARMACY AND APPLIED LIFE SCIENCES   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c RIKEN HARIMA INSTITUTE   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

CCA sequence; Pre tRNA; Pyrobaculum aerophilum; Thermoplasma acidophilum; Thermotoga maritima; Thermus thermophilus; tRNA 3 processing; tRNase Z

Indexed keywords

BACTERIAL PROTEIN; HISTIDINE; METAL; RIBONUCLEASE; TRANSFER RIBONUCLEASE Z; TRANSFER RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BACILLUS SUBTILIS; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ISOLATION; ENZYME SUBSTRATE; EUBACTERIUM; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DEGRADATION; PROTEIN ISOLATION; PYROBACULUM; THERMOPLASMA ACIDOPHILUM; THERMOTOGA MARITIMA; THERMUS THERMOPHILUS;

AMINO ACID SEQUENCE; BACTERIA; BINDING SITES; DROSOPHILA PROTEINS; ENDORIBONUCLEASES; ENZYME ACTIVATION; ENZYME STABILITY; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SPECIES SPECIFICITY; SUBSTRATE SPECIFICITY; TEMPERATURE;

ARCHAEA; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); PROKARYOTA; PYROBACULUM; PYROBACULUM AEROPHILUM; THERMOPLASMA ACIDOPHILUM; THERMOTOGA MARITIMA; THERMUS THERMOPHILUS;

EID: 33646402107     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.04.105     Document Type: Article

References (27)

1. Sprinzl M., Horn C., Brown M., Ioudovitch A., and Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26 (1998) 148-153
2. Tamura K., Nameki N., Hasegawa T., Shimizu M., and Himeno H. Role of the CCA terminal sequence of tRNA(Val) in aminoacylation with valyl-tRNA synthetase. J. Biol. Chem. 269 (1994) 22173-22177
3. Green R., and Noller H.F. Ribosomes and translation. Annu. Rev. Biochem. 66 (1997) 679-716
4. Schurer H., Schiffer S., Marchfelder A., and Mörl M. This is the end: processing, editing and repair at the tRNA 3′-terminus. Biol. Chem. 382 (2001) 1147-1156
5. Nashimoto M. Distribution of both lengths and 5′ terminal nucleotides of mammalian pre-tRNA 3′ trailers reflects properties of 3′ processing endoribonuclease. Nucleic Acids Res. 25 (1997) 1148-1155
6. Schiffer S., Rosch S., and Marchfelder A. Assigning a function to a conserved group of proteins: the tRNA 3′-processing enzymes. EMBO J. 21 (2002) 2769-2777
7. Takaku H., Minagawa A., Takagi M., and Nashimoto M. A candidate prostate cancer susceptibility gene encodes tRNA 3′ processing endoribonuclease. Nucleic Acids Res. 31 (2003) 2272-2278
8. Pellegrini O., Nezzar J., Marchfelder A., Putzer H., and Condon C. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 22 (2003) 4534-4543
9. Minagawa A., Takaku H., Takagi M., and Nashimoto M. A novel endonucleolytic mechanism to generate the CCA 3′ termini of tRNA molecules in Thermotoga maritima. J. Biol. Chem. 279 (2004) 15688-15697
10. Dubrovsky E.B., Dubrovskaya V.A., Levinger L., Schiffer S., and Marchfelder A. Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3′ ends in vivo. Nucleic Acids Res. 32 (2004) 255-262
11. Takaku H., Minagawa A., Takagi M., and Nashimoto M. The N-terminal half domain of the long form of tRNase Z is required for the RNase 65 activity. Nucleic Acids Res. 32 (2004) 4429-4438
12. Zareen N., Yan H., Hopkinson A., and Levinger L. Residues in the conserved His domain of fruit fly tRNase Z that function in catalysis are not involved in substrate recognition or binding. J. Mol. Biol. 350 (2005) 189-199
13. Ishii R., Minagawa A., Takaku H., Takagi M., Nashimoto M., and Yokoyama S. Crystal structure of the tRNA 3′ processing endoribonuclease tRNase Z from Thermotoga maritima. J. Biol. Chem. 280 (2005) 14138-14144
14. de la Sierra-Gallay I.L., Pellegrini O., and Condon C. Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 433 (2005) 657-661
15. Schilling O., Säpth B., Kostelecky B., Marchfelder A., Meyer-Klaucke W., and Vogel A. Exosite modules guide substrate recognition in the ZiPD/ElaC protein family. J. Biol. Chem. 280 (2005) 17857-17862
16. Li Z., and Deutscher M.P. Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo. Cell 86 (1996) 503-512
17. Schilling O., Ruggeberg S., Vogel A., Rittner N., Weichert S., Schmidt S., et al. Characterization of an Escherichia coli elaC deletion mutant. Biochem. Biophys. Res. Commun. 320 (2004) 1365-1373
18. Wen T., Oussenko I.A., Pellegrini O., Bechhofer D.H., and Condon C. Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis. Nucleic Acids Res. 33 (2005) 3636-3643
19. Holm L., and Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26 (1998) 316-319
20. Nashimoto M., Wesemann D.R., Geary S., Tamura M., and Kaspar R.L. Long 5′ leaders inhibit removal of a 3′ trailer from a precursor tRNA by mammalian tRNA 3′ processing endoribonuclease. Nucleic Acids Res. 27 (1999) 2770-2776
21. Nashimoto M., Tamura M., and Kaspar R.L. Selection of cleavage site by mammalian tRNA 3′ processing endoribonuclease. J. Mol. Biol. 287 (1999) 727-740
22. Nashimoto M., Tamura M., and Kaspar R.L. Minimum requirements for substrates of mammalian tRNA 3′ processing endoribonuclease. Biochemistry 38 (1999) 12089-12096
23. Nashimoto M., Nashimoto C., Tamura M., Kaspar R.L., and Ochi K. The inhibitory effect of the autoantigen La on in vitro 3′ processing of mammalian precursor tRNA. J. Mol. Biol. 312 (2001) 975-984
24. Daiyasu H., Osaka K., Ishino Y., and Toh H. Expansion of the zinc metallo-hydrolase family of the β-lactamase fold. FEBS Lett. 503 (2001) 1-6
25. Gesteland R.F., Cech T., and Atkins J.F. The RNA World. second ed. (1999), Cold Spring Harbor Laboratory Press, New York
26. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
27. Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308