Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z

Nature

Volumn 433, Issue 7026, 2005, Pages 657-661

  De La Sierra Gallay, Inés Li ^b   Pellegrini, Olivier ^a   Condon, Ciarán ^a  

^a CNRS   (France)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CRYSTAL STRUCTURE; ENZYME INHIBITION; ENZYMES; RNA;

ALLOSTERY; LIVING ORGANISMS; RIBOZYME; SUBSTRATE BINDING;

SUBSTRATES;

AMINO ACID TRANSFER RNA LIGASE; BETA LACTAMASE; HYDROLASE; NUCLEOTIDYLTRANSFERASE; RIBONUCLEASE; RIBONUCLEASE P; RIBONUCLEASE Z; RIBOZYME; RNA PRECURSOR; TRANSFER RNA; UNCLASSIFIED DRUG; RNASE Z; ZINC;

RNA;

ALLOSTERISM; ARTICLE; BACILLUS SUBTILIS; BASE PAIRING; CONTROLLED STUDY; COVALENT BOND; CRYSTAL STRUCTURE; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; HYDROLYSIS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; RNA CLEAVAGE; SEQUENCE HOMOLOGY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRICITY; ENZYMOLOGY; ESCHERICHIA COLI; METABOLISM; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION; THERMOTOGA MARITIMA; X RAY CRYSTALLOGRAPHY;

BACILLUS SUBTILIS; POSIBACTERIA;

ALLOSTERIC REGULATION; BACILLUS SUBTILIS; BETA-LACTAMASES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; ENDORIBONUCLEASES; ESCHERICHIA COLI; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; THERMOTOGA MARITIMA; ZINC;

EID: 14144251951     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03284     Document Type: Article

References (29)

1. Frank, D. N. & Pace, N. R. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67, 153-180 (1998).
2. Garber, R. L. & Altman, S. In vitro processing of B. mori transfer RNA precursor molecules. Cell 17, 389-397 (1979).
3. Li, Z. & Deutscher, M. P. Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo. Cell 86, 503-512 (1996).
4. Garber, R. L. & Gage, L. P. Transcription of a cloned Bombyx mori tRNA2Ala gene: nucleotide sequence of the tRNA precursor and its processing in vitro. Cell 18, 817-828 (1979).
5. Schiffer, S., Rosch, S. & Marchfelder, A. Assigning a function to a conserved group of proteins: the tRNA 3′-processing enzymes. EMBO J. 21, 2769-2777 (2002).
6. 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, 1148-1154 (1997).
7. Kunzmann, A., Brennicke, A. & Marchfelder, A. 5′ end maturation and RNA editing have to precede tRNA 3′ processing in plant mitochondria. Proc. Natl Acad. Sci. USA 95, 108-113 (1998).
8. Schierling, K., Rosch, S., Rupprecht, R., Schiffer, S. & Marchfelder, A. tRNA 3′ end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii. J. Mol. Biol. 316, 895-902 (2002).
9. Pellegrini, O., Nezzar, J., Marchfelder, A., Putzer, H, & Condon, C. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 22, 4534-4543 (2003).
10. Tavtigian, S. V. et al. A candidate prostate cancer susceptibility gene at chromosome 17p. Nature Genet. 27, 172-180 (2001).
11. Minagawa, A., Takaku, H., Takagi, M. & Nashimoto, M. A novel endonucleolytic mechanism to generate the CCA 3′ termini of tRNA molecules in Thermotoga maritima. J. Biol. Chem. 279, 15688-15697 (2004).
12. Mohan, A., Whyte, S., Wang, X., Nashimoto, M. & Levinger, L. The 3′ end CCA of mature tRNA is an antideterminant for eukaryotic 3′-tRNase. RNA 5, 245-256 (1999).
13. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
14. Schiffer, S., Helm, M., Theobald-Dietrich, A., Giege, R. & Marchfelder, A. The plant tRNA 3′ processing enzyme has a broad substrate spectrum. Biochemistry 40, 8264-8272 (2001).
15. Cameron, A. D., Ridderstrom, M., Olin, B. & Mannervik, B. Crystal structure of human glyoxalase II and its compiex with a glutathione thioiester substrate analogue. Struct. Fold. Des. 7, 1067-1078 (1999).
16. Nashimoto, M., Wesemann, D. R., Geary, S., Tamura, M. & 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, 2770-2776 (1999).
17. Vogel, A., Schilling, O., Niecke, M., Bettmer, J. & Meyer-Klaucke, W. ElaC encodes a novel binuclear zinc phosphodiesterase. J. Biol. Chem. 277, 29078-29085 (2002).
18. Daiyasu, H., Osaka, K., Ishino, Y. & Toh, H. Expansion of the zinc metalJo-hydrolase family of the β-lactamase fold. FEBS Lett. 503, 1-6 (2001).
19. Carfi, A. et al. The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold. EMBO J. 14, 4914-4921 (1995).
20. Frazao, C. et al. Structure of a dioxygen reduction enzyme from Desulfovibrio gigas. Nature Struct. Biol. 7, 1041-1045 (2000).
21. Matthews, B. W. Solvent content of protein crystals. J. Mol. Biol. 33, 491-497 (1968).
22. CCP4. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
23. Otwinowski, Z. & Minor, W. in Methods in Enzymology Vol. 276, Macromolecuiar Crystallography Part A (eds Carter, C. W. Jr & Sweet, R. M.) 307-326 (Academic, New York, 1997).
24. Uson, I. & Sheldrick, G. M. Advances in direct methods for protein crystallography. Curr. Opin. Struct. Biol. 9, 643-648 (1999).
25. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772-1779 (2002).
26. Lu, G. FINDNCS: A program to detect non-crystallographic symmetries in protein crystals from heavy atom sites. J. Appl. Crystallogr. 32, 365-368 (1999).
27. Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463 (1999).
28. Kleywegt, G. J. & Jones, T. A. in From First Map to Final Model (eds Bailey, S. R. H. & Waller, D.) 59-66 (SERC Daresbury Laboratory, Daresbury, UK, 1994).
29. Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).