Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma

Nature

Volumn 462, Issue 7274, 2009, Pages 808-812

  Guo, Min ^a   Chong, Yeeting E ^a   Shapiro, Ryan ^a   Beebe, Kirk ^a,b   Yang, Xiang Lei ^a   Schimmel, Paul ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b METABOLON INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE PHOSPHATE; ALANINE; ALANINE TRANSFER RNA LIGASE; ALPHA AMINO ACID; AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; SERINE;

AMINO ACID; BACTERIUM; GENETIC ANALYSIS; GENOME; PROTEIN; REACTION KINETICS; RODENT;

ADENYLATION; AMINOACYLATION; ARTICLE; CHEMICAL ANALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; GENOME; KINETICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN SYNTHESIS; RNA EDITING; RNA TRANSLATION;

ALANINE; ALANINE-TRNA LIGASE; ASPARTIC ACID; CATALYTIC DOMAIN; CRYSTALLIZATION; ESCHERICHIA COLI; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; RNA, TRANSFER, ALA; SERINE; STRUCTURE-ACTIVITY RELATIONSHIP;

MUS;

EID: 72049087000     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08612     Document Type: Article

References (34)

1. Beebe, K., Ribas De Pouplana, L. & Schimmel, P. Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J. 22, 668-675 (2003).
2. Lee, J. W. et al. Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443, 50-55 (2006).
3. Beebe, K., Mock, M., Merriman, E. & Schimmel, P. Distinct domains of tRNA synthetase recognize the same base pair. Nature 451, 90-93 (2008).
4. Carter, C. W. Jr. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu. Rev. Biochem. 62, 715-748 (1993).
5. Giege, R. The early history of tRNA recognition by aminoacyl-tRNA synthetases. J. Biosci. 31, 477-488 (2006).
6. Norris, A. T. & Berg, P. Mechanism of aminoacyl RNA synthesis: studies with isolated aminoacyl adenylate complexes of isoleucyl RNA synthetase. Proc. Natl Acad. Sci. USA 52, 330-337 (1964).
7. Eldred, E. W. & Schimmel, P. R. Rapid deacylation by isoleucyl transfer ribonucleic acid synthetase of isoleucine-specific transfer ribonucleic acid aminoacylated with valine. J. Biol. Chem. 247, 2961-2964 (1972).
8. Boniecki, M. T., Vu, M. T., Betha, A. K. & Martinis, S. A. CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase. Proc. Natl Acad. Sci. USA 105, 19223-19228 (2008)
9. Fersht, A. R. Enzyme Structure and Mechanism (Freeman, 1977).
10. Nureki, O. et al. Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases. Cold Spring Harb. Symp. Quant. Biol. 66, 167-173 (2001).
11. Fersht, A. R. Sieves in sequence. Science 280, 541 (1998).
12. Fukai, S. et al. Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNAVal and valyl-tRNA synthetase. Cell 103, 793-803 (2000).
13. Tsui, W. C. & Fersht, A. R. Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli. Nucleic Acids Res. 9, 4627-4637 (1981).
14. Ahel, I., Korencic, D., Ibba, M. & Söll, D. Trans-editing of mischarged tRNAs. Proc. Natl Acad. Sci. USA 100, 15422-15427 (2003).
15. Chong, Y. E., Yang, X. L. & Schimmel, P. Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation. J. Biol. Chem. 283, 30073-30078 (2008).
16. Ling, J. et al. Resampling and editing of mischarged tRNA prior to translation elongation. Mol. Cell 33, 654-660 (2009).
17. Guo, M. et al. The C-Ala domain brings together editing and aminoacylation functions on one tRNA. Science 325, 744-747 (2009).
18. Sokabe, M., Okada, A., Yao, M., Nakashima, T. & Tanaka, I. Molecular basis of alanine discrimination in editing site. Proc. Natl Acad. Sci. USA 102, 11669-11674 (2005).
19. Ho, B. K. & Gruswitz, F. HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct. Biol. 8, 49 (2008).
20. Arnez, J. G. & Moras, D. Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci. 22, 211-216 (1997).
21. Davis, M. W., Buechter, D. D. & Schimmel, P. Functional dissection of a predicted class-defining motif in a class II tRNA synthetase of unknown structure. Biochemistry 33, 9904-9911 (1994).
22. Jakubowski, H. in The Aminoacyl-tRNA Synthetases (eds Ibba, M., Francklyn, C. & Cusack, S.) 384-396 (Eurekah, 2005).
23. Shi, J. P., Musier-Forsyth, K. & Schimmel, P. Region of a conserved sequence motif in a class II tRNA synthetase needed for transfer of an activated amino acid to an RNA substrate. Biochemistry 33, 5312-5318 (1994).
24. Tyr by tyrosyl-tRNA synthetase. J. Mol. Biol. 303, 299-310 (2000).
25. Sankaranarayanan, R. et al. Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nature Struct. Biol. 7, 461-465 (2000).
26. First, E. A. in The Aminoacyl-tRNA Synthetases (eds Ibba, M., Francklyn, C. & Cusack, S.) 328-352 (Eurekah, 2005).
27. Belrhali, H. et al. Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science 263, 1432-1436 (1994).
28. Cieslik, M. & Derewenda, Z. S. The role of entropy and polarity in intermolecular contacts in protein crystals. Acta Crystallogr. D 65, 500-509 (2009).
29. Itoh, Y. et al. Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. RNA Biol. 5, 169-177 (2008).
30. Swairjo, M. A. & Schimmel, P. R. Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc. Natl Acad. Sci. USA 102, 988-993 (2005).
31. Malde, A. K. & Mark, A. E. Binding and enantiomeric selectivity of threonyl-tRNA synthetase. J. Am. Chem. Soc. 131, 3848-3849 (2009).
32. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997)
33. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
34. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).