Mutation and evolution of the magnesium-binding site of a class II aminoacyl-tRNA synthetase

Biochemistry

Volumn 43, Issue 22, 2004, Pages 7028-7037

  Ador, Laurent ^a   Jaeger, Sophie ^a   Geslain, Renaud ^a   Martin, Franck ^a   Cavarelli, Jean ^b   Eriani, Gilbert ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

^b INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ANALYSIS; ADENOSINETRIPHOSPHATE; AMINO ACIDS; CATALYSIS; MAGNESIUM PRINTING PLATES; MUTAGENESIS; RNA;

AMINOACYLATION REACTIONS; ELECTROPOSITIVITY;

BIOCHEMISTRY;

ADENOSINE TRIPHOSPHATE; AMINO ACID TRANSFER RNA LIGASE; ASPARTATE TRANSFER RNA LIGASE; ASPARTIC ACID; FUNGAL ENZYME; MAGNESIUM ION; SINGLE STRANDED DNA;

ARTICLE; BACTERIUM; BINDING SITE; ENZYME BINDING; EVOLUTION; GENE OVEREXPRESSION; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; SITE DIRECTED MUTAGENESIS; YEAST;

ACYLATION; ADENOSINE TRIPHOSPHATE; AMINO ACID SUBSTITUTION; ASPARTATE-TRNA LIGASE; ASPARTIC ACID; BINDING SITES; CATALYTIC DOMAIN; CELL DEATH; COMBINATORIAL CHEMISTRY TECHNIQUES; EVOLUTION, MOLECULAR; KINETICS; MAGNESIUM; MUTAGENESIS, SITE-DIRECTED; MUTATION; PEPTIDE LIBRARY; PROTEIN BINDING; PROTEIN CONFORMATION; RNA, TRANSFER, ASP; SACCHAROMYCES CEREVISIAE; TRANSFECTION;

BACTERIA (MICROORGANISMS); SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 2642524472     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049617+     Document Type: Article

References (35)

1. Eriani, G., Delarue, M., Poch, O., Gangloff, J., and Moras, D. (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs, Nature 347, 203-206.
2. Asp in Escherichia coli - a snapshot of the second step, EMBO J. 18, 6532-6541.
3. Perona, J. J., Rould, M. A., and Steitz, T. A. (1993) Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase, Biochemistry 32, 8758-8771.
4. Cavarelli, J., Eriani, G., Rees, B., Ruff, M., Boeglin, M., Mitschler, A., Martin, F., Gangloff, J., Thierry, J. C., and Moras, D. (1994) The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction, EMBO J. 13, 327-337.
5. Asp, Science 252, 1682-1689.
6. Poterszman, A., Delarue, M., Thierry, J.-C., and Moras, D. (1994) Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase, J. Mol. Biol. 244, 158-167.
7. Cavarelli, J., Rees, B., Ruff, M., Poterszman, A., Thierry, J.-C., and Moras, D. (1992) in Structural Tools for the Analysis of Protein-Nucleic Acid Complexes, pp 287-298, Birkhäuser Verlag, Basel.
8. Asp by aspartyl-tRNA synthetase, J. Mol. Biol. 299, 1051-1060.
9. Asp complex reveals a tRNA-dependent control mechanism, EMBO J. 20, 5290-5301.
10. Asp-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain, J. Mol. Biol. 299, 1333-1344.
11. Rees, B., Webster, G., Delarue, M., Boeglin, M., and Moras, D. (2000) Aspartyl tRNA-synthetase from Escherichia coli: Flexibility and adaptability to the substrates, J. Mol. Biol. 299, 1157-1164.
12. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J. C., and Moras, D. (1998) Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation, EMBO J. 17, 5227-5237.
13. Belrhali, H., Yaremchuk, A., Tukalo, M., Berthet-Colominas, C., Rasmussen, B., Bösecke, P., Diat, O., and Cusack, S. (1995) The structural basis for seryl-adenylate and Ap4A synthesis by seryl-tRNA synthetase, Structure 3, 341-352.
14. Amez, J. G., Augustine, J. G., Moras, D., and Francklyn, C. S. (1997) The first step of aminoacylation at the atomic level in hisfidyl-tRNA synthetase, Proc. Natl. Acad. Sci. U.S.A. 94, 7144-7149.
15. Patterson, T. A., Costantino, N., Dasgupta, S., and Court, D. L. (1993) Improved bacterial hosts for regulated expression of genes from λ PL plasmid vectors, Gene 132, 83-87.
16. Ador, L., Camasses, A., Erbs, P., Cavarelli, J., Moras, D., Gangloff, J., and Eriani, G. (1999) Active site mapping of yeast aspartyl-tRNA synthetase by in vivo selection of enzyme mutations lethal for cell growth, J. Mol. Biol. 288, 231-242.
17. Sellami, M., Chatton, B., Fasiolo, F., Dirheimer, G., and Gangloff, J. (1986) Nucleotide sequence of the gene coding for yeast cytoplasmic aspartyl-tRNA synthetase (APS); mapping of the 5′ and 3′ termini of AspRS mRNA, Nucleic Acids Res. 14, 1657-1666.
18. Sikorski, R. S., and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae, Genetics 122, 19-27.
19. Mumberg, D., Muller, R., and Funk, M. (1994) Regulatable promoters of Saccharomyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression, Nucleic Acids Res. 22, 5767-4768.
20. Alexeyev, M. F. (1995) Three kanamycin resistance gene cassettes with different polylinkers, Biotechniques 18, 52-56.
21. Koshland, D., Kent, J. C., and Hartwell, L. H. (1985) Genetic analysis of the mitotic transmission of minichromosomes, Cell 40, 393-403.
22. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Smith, J. A., Seidman, J. G., and Struhl, K. (1987) Current Protocols in Molecular Biology, Wiley-Interscience, New York.
23. Kunkel, T. A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection, Proc. Natl. Acad. Sci. U.S.A. 82, 488-492.
24. Asp binding in the ground and transition-state complex and discriminate against non-cognate tRNAs, J. Mol. Biol. 291, 761-773.
25. Boeke, J. D., LaCroute, F., and Fink, G. R. (1984) A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance, Mol. Gen. Genet. 197, 345-346.
26. Courtney, M., Buchwalder, A., Tessier, L. H., Jaye, M., Benavente, A., Balland, A., Kohli, V., Lathe, R., Tolstoshev, P., and Lecocq, J. P. (1984) High-level production of biologically active human α1-antitrypsin in Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 81, 669-673.
27. Prévost, G., Eriani, G., Kern, D., Dirheimer, G., and Gangloff, J. (1989) Study of the arrangement of the functional domains along the cytoplasmic aspartyl-tRNA synthetase, Eur. J. Biochem. 180, 351-358.
28. Eriani, G., Cavarelli, J., Martin, F., Dirheimer, G., Moras, D., and Gangloff, J. (1993) Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline, Proc. Natl. Acad. Sci. U.S.A. 90, 10816-10820.
29. Eriani, G., Prevost, G., Kern, D., Vincendon, P., Dirheimer, G., and Gangloff, J. (1991) Cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae. Study of its functional organisation by deletion analysis, Eur. J. Biochem. 200, 337-343.
30. Berthet-Colominas, C., Seignovert, L., Hartlein, M., Grotli, M., Cusack, S., and Leberman, R. (1998) The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid, EMBO J. 17, 2947-2960.
31. Desogus, G., Todone, F., Brick, P., and Onesti, S. (2000) Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction, Biochemistry 39, 8418-8425.
32. Airas, R. K. (1996) Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli, Eur. J. Biochem. 240, 223-231.
33. Aberg, A., Yaremchuk, A., Tukalo, M., Rasmussen, B., and Cusack, S. (1997) Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase, Biochemistry 36, 3084-3094.
34. 2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments, Proteins 32, 362-380.
35. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, on the World Wide Web, http://www.pymol.org.