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

Abstract

Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences1,2,3. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly1,2. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps—free-standing, genome-encoded editing proteins that clear Ser-tRNAAla. The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the α-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.

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Figure 1: Plasticity of active site in AlaRS.
Figure 2: Alanine active site with intrinsic design defect that mis-binds serine.
Figure 3: Mutant enzyme with a smaller pocket retains serine binding affinity.
Figure 4: Critical role of Asp 235 shows dilemma for AlaRSs.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited with the Protein Data Bank under accession codes 3hxu (WT/Ala-SA), 3hxv (WT/Gly-SA), 3hxw (WT/Ser-SA), 3hxx (WT/AMP-PCP/Mg(II)), 3hxy (WT/Ala-AMP/PCP/AMP-PCP/Mg(II)), 3hxz (G237A/Ala-SA), 3hy0 (G237A/Gly-SA) and 3hy1 (G237A-apo and G237A/Ser-SA).

References

  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)

    Article  CAS  Google Scholar 

  2. Lee, J. W. et al. Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443, 50–55 (2006)

    Article  ADS  CAS  Google Scholar 

  3. Beebe, K., Mock, M., Merriman, E. & Schimmel, P. Distinct domains of tRNA synthetase recognize the same base pair. Nature 451, 90–93 (2008)

    Article  ADS  CAS  Google Scholar 

  4. Carter, C. W. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu. Rev. Biochem. 62, 715–748 (1993)

    Article  CAS  Google Scholar 

  5. Giege, R. The early history of tRNA recognition by aminoacyl-tRNA synthetases. J. Biosci. 31, 477–488 (2006)

    Article  CAS  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  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)

    CAS  PubMed  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  9. Fersht, A. R. Enzyme Structure and Mechanism (Freeman, 1977)

    Google Scholar 

  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)

    Article  CAS  Google Scholar 

  11. Fersht, A. R. Sieves in sequence. Science 280, 541 (1998)

    Article  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  14. Ahel, I., Korencic, D., Ibba, M. & Söll, D. Trans-editing of mischarged tRNAs. Proc. Natl Acad. Sci. USA 100, 15422–15427 (2003)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  16. Ling, J. et al. Resampling and editing of mischarged tRNA prior to translation elongation. Mol. Cell 33, 654–660 (2009)

    Article  CAS  Google Scholar 

  17. Guo, M. et al. The C-Ala domain brings together editing and aminoacylation functions on one tRNA. Science 325, 744–747 (2009)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  19. Ho, B. K. & Gruswitz, F. HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct. Biol. 8, 49 (2008)

    Article  Google Scholar 

  20. Arnez, J. G. & Moras, D. Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci. 22, 211–216 (1997)

    Article  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  22. Jakubowski, H. in The Aminoacyl-tRNA Synthetases (eds Ibba, M., Francklyn, C. & Cusack, S.) 384–396 (Eurekah, 2005)

    Google Scholar 

  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)

    Article  CAS  Google Scholar 

  24. Xin, Y., Li, W. & First, E. A. Stabilization of the transition state for the transfer of tyrosine to tRNATyr by tyrosyl-tRNA synthetase. J. Mol. Biol. 303, 299–310 (2000)

    Article  CAS  Google Scholar 

  25. Sankaranarayanan, R. et al. Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nature Struct. Biol. 7, 461–465 (2000)

    Article  CAS  Google Scholar 

  26. First, E. A. in The Aminoacyl-tRNA Synthetases (eds Ibba, M., Francklyn, C. & Cusack, S.) 328–352 (Eurekah, 2005)

    Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  29. Itoh, Y. et al. Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii . RNA Biol. 5, 169–177 (2008)

    Article  CAS  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  31. Malde, A. K. & Mark, A. E. Binding and enantiomeric selectivity of threonyl-tRNA synthetase. J. Am. Chem. Soc. 131, 3848–3849 (2009)

    Article  CAS  Google Scholar 

  32. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  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)

    Article  Google Scholar 

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Acknowledgements

We thank R. J. Read for pointing out the errors in the previous AlaRS–ligand structures and for crystallographic discussions; and G. J. Kleywegt, Z. Otwinowski and A. Perrakis for technical assistance. X-ray diffraction data were collected at Stanford Synchrotron Radiation Laboratory (SSRL) beamlines 7-1, 9-1 and 11-1. This work was supported by grant GM 15539 from the National Institutes of Health and by a fellowship from the National Foundation for Cancer Research.

Author Contributions M.G., X.-L.Y. and P.S. designed the experiments. M.G., Y.E.C., R.S. and K.B. performed the experiments. M.G. and Y.E.C. analysed the data. M.G., Y.E.C., X.-L.Y. and P.S. wrote the paper. All authors discussed the results and commented on the manuscript.

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Correspondence to Paul Schimmel.

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Supplementary Figures

This file contains Supplementary Figures 1-8 with Legends. (PDF 5485 kb)

Supplementary Table 1

This file contains a summary of the data collection and refinement statistics of the nine structures. (PDF 192 kb)

Supplementary Movie 1

This movie file shows that serine paradox is caused by AlaRS recognition dilemma (see Supplementary Figures file for full Legend). (MOV 6540 kb)

Supplementary Movie 2

This movie file shows the alanyl-adenylate formation mechanism (see Supplementary Figures file for full Legend). (MOV 4436 kb)

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Guo, M., Chong, Y., Shapiro, R. et al. Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature 462, 808–812 (2009). https://doi.org/10.1038/nature08612

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