The Flexible Arm of tRNase Z Is Not Essential for Pre-tRNA Binding but Affects Cleavage Site Selection

Journal of Molecular Biology

Volumn 381, Issue 2, 2008, Pages 289-299

  Minagawa, Asako ^a   Ishii, Ryohei ^b   Takaku, Hiroaki ^a   Yokoyama, Shigeyuki ^b,c   Nashimoto, Masayuki ^a  

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

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

cleavage site selection; flexible arm; pre tRNA; tRNA 3 processing endoribonuclease; tRNase Z

Indexed keywords

ENZYME; NUCLEOTIDE; TRANSFER RNA; TRNASE Z;

ARTICLE; BACILLUS SUBTILIS; ENZYME ACTIVITY; NONHUMAN; PRIORITY JOURNAL; RNA BINDING; THERMOTOGA MARITIMA;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); THERMOTOGA MARITIMA;

EID: 47049123151     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.05.016     Document Type: Article

References (23)

1. 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
2. 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
3. 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
4. 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
5. Späth B., Kirchner S., Vogel A., Schubert S., Meinlschmidt P., Aymanns S., et al. Analysis of the functional modules of the tRNA 3′ endonuclease (tRNase Z). J. Biol. Chem. 280 (2005) 35440-35447
6. Minagawa A., Takaku H., Shibata H.S., Ishii R., Takagi M., Yokoyama S., and Nashimoto M. Substrate recognition ability differs among various prokaryotic tRNase Zs. Biochem. Biophys. Res. Commun. 345 (2006) 385-393
7. 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
8. 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
9. 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
10. Kostelecky B., Pohl E., Vogel A., Schilling O., and Meyer-Klaucke W. The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins. J. Bacteriol. 188 (2006) 1607-1614
11. 2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis. Nucleic Acids Res. 34 (2006) 3811-3818
12. 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
13. Nashimoto M., Tamura M., and Kaspar R.L. Minimum requirements for substrates of mammalian tRNA 3′ processing endoribonuclease. Biochemistry 38 (1999) 12089-12096
14. Schilling O., Späth 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
15. de la Sierra-Gallay I.L., Mathy N., Pellegrini O., and Condon C. Structure of the ubiquitous 3′ processing enzyme RNase Z bound to transfer RNA. Nat. Struct. Mol. Biol. 13 (2006) 376-377
16. Ishii R., Minagawa A., Takaku H., Takagi M., Nashimoto M., and Yokoyama S. The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes. Acta Crystallogr. F 63 (2007) 637-641
17. 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
18. Shibata H.S., Minagawa A., Takaku H., Takagi M., and Nashimoto M. Unstructured RNA is a substrate for tRNase Z. Biochemistry 45 (2006) 5486-5492
19. Arg is essential for in vitro specific cleavage of partially synthesized mouse 18S rRNA. Nucleic Acids Res. 21 (1993) 4696-4702
20. Nashimoto M. Conversion of mammalian tRNA 3′ processing endoribonuclease to four-base-recognizing RNA cutters. Nucleic Acids Res. 23 (1995) 3642-3647
21. 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 tRNAs. J. Mol. Biol. 312 (2001) 975-984
22. Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., and Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77 (1989) 51-59
23. Shibata H.S., Takaku H., Takagi M., and Nashimoto M. The T loop structure is dispensable for substrate recognition by tRNase ZL. J. Biol. Chem. 280 (2005) 22326-22334