Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality

Abstract

Protein multifunctionality is an emerging explanation for the complexity of higher organisms. In this regard, aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, but some also act in pathways for inflammation, angiogenesis and apoptosis. It is unclear how these multiple functions evolved and how they relate to the active site. Here structural modeling analysis, mutagenesis and cell-based functional studies show that the potent angiostatic, natural fragment of human tryptophanyl-tRNA synthetase (TrpRS) associates via tryptophan side chains that protrude from its cognate cellular receptor vascular endothelial cadherin (VE-cadherin). VE-cadherin's tryptophan side chains fit into the tryptophan-specific active site of the synthetase. Thus, specific side chains of the receptor mimic amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multifunctionality of human tRNA synthetases and other proteins.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Hypothesized mode of binding of T2-TrpRS to VE-cadherin.
Figure 2: Comparison of FL-TrpRS and T2-TrpRS for VE-cadherin−binding ability and angiostatic activity.
Figure 3: Trp-SA inhibits the T2-TrpRS−VE-cadherin interaction and the angiostatic activity of T2-TrpRS.
Figure 4: Mutagenesis studies confirming that the mechanism for T2-TrpRS's angiostatic activity involves the tryptophan and adenosine pockets of T2-TrpRS, as well as Trp2 and Trp4 of VE-cadherin.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Hausmann, C.D. & Ibba, M. Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed. FEMS Microbiol. Rev. 32, 705–721 (2008).

    Article  CAS  Google Scholar 

  2. Park, S.G., Ewalt, K.L. & Kim, S. Functional expansion of aminoacyl-tRNA synthetases and their interacting factors: new perspectives on housekeepers. Trends Biochem. Sci. 30, 569–574 (2005).

    Article  CAS  Google Scholar 

  3. Giege, R. Toward a more complete view of tRNA biology. Nat. Struct. Mol. Biol. 15, 1007–1014 (2008).

    Article  CAS  Google Scholar 

  4. Paukstelis, P.J. et al. Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA. Nature 451, 94–97 (2008).

    Article  CAS  Google Scholar 

  5. Rho, S.B., Lincecum, T.L. Jr. & Martinis, S.A. An inserted region of leucyl-tRNA synthetase plays a critical role in group I intron splicing. EMBO J. 21, 6874–6881 (2002).

    Article  CAS  Google Scholar 

  6. Jia, J., Arif, A., Ray, P.S. & Fox, P.L. WHEP domains direct noncanonical function of glutamyl-prolyl tRNA synthetase in translational control of gene expression. Mol. Cell 29, 679–690 (2008).

    Article  CAS  Google Scholar 

  7. Lee, Y.N., Nechushtan, H., Figov, N. & Razin, E. The function of lysyl-tRNA synthetase and Ap4A as signaling regulators of MITF activity in FcepsilonRI-activated mast cells. Immunity 20, 145–151 (2004).

    Article  CAS  Google Scholar 

  8. Sampath, P. et al. Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation. Cell 119, 195–208 (2004).

    Article  CAS  Google Scholar 

  9. Kise, Y. et al. A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase. Nat. Struct. Mol. Biol. 11, 149–156 (2004).

    Article  CAS  Google Scholar 

  10. Otani, A. et al. Bone marrow-derived stem cells target retinal astrocytes and can promote or inhibit retinal angiogenesis. Nat. Med. 8, 1004–1010 (2002).

    Article  CAS  Google Scholar 

  11. Otani, A. et al. A fragment of human TrpRS as a potent antagonist of ocular angiogenesis. Proc. Natl. Acad. Sci. USA 99, 178–183 (2002).

    Article  CAS  Google Scholar 

  12. Wakasugi, K. & Schimmel, P. Two distinct cytokines released from a human aminoacyl-tRNA synthetase. Science 284, 147–151 (1999).

    Article  CAS  Google Scholar 

  13. Wakasugi, K. et al. Induction of angiogenesis by a fragment of human tyrosyl-tRNA synthetase. J. Biol. Chem. 277, 20124–20126 (2002).

    Article  CAS  Google Scholar 

  14. Wakasugi, K. et al. A human aminoacyl-tRNA synthetase as a regulator of angiogenesis. Proc. Natl. Acad. Sci. USA 99, 173–177 (2002).

    Article  CAS  Google Scholar 

  15. Park, S.G. et al. Human lysyl-tRNA synthetase is secreted to trigger proinflammatory response. Proc. Natl. Acad. Sci. USA 102, 6356–6361 (2005).

    Article  CAS  Google Scholar 

  16. Howard, O.M. et al. Histidyl-tRNA synthetase and asparaginyl-tRNA synthetase, autoantigens in myositis, activate chemokine receptors on T lymphocytes and immature dendritic cells. J. Exp. Med. 196, 781–791 (2002).

    Article  CAS  Google Scholar 

  17. Ko, Y.G. et al. Glutamine-dependent antiapoptotic interaction of human glutaminyl-tRNA synthetase with apoptosis signal-regulating kinase 1. J. Biol. Chem. 276, 6030–6036 (2001).

    Article  CAS  Google Scholar 

  18. Javanbakht, H. et al. The interaction between HIV-1 Gag and human lysyl-tRNA synthetase during viral assembly. J. Biol. Chem. 278, 27644–27651 (2003).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  20. Nangle, L.A. et al. Charcot-Marie-Tooth disease-associated mutant tRNA synthetases linked to altered dimer interface and neurite distribution defect. Proc. Natl. Acad. Sci. USA 104, 11239–11244 (2007).

    Article  CAS  Google Scholar 

  21. Park, S.G., Schimmel, P. & Kim, S. Aminoacyl tRNA synthetases and their connections to disease. Proc. Natl. Acad. Sci. USA 105, 11043–11049 (2008).

    Article  CAS  Google Scholar 

  22. Seburn, K.L. et al. An active dominant mutation of glycyl-tRNA synthetase causes neuropathy in a Charcot-Marie-Tooth 2D mouse model. Neuron 51, 715–726 (2006).

    Article  CAS  Google Scholar 

  23. Yang, X.L. et al. Gain-of-function mutational activation of human tRNA synthetase procytokine. Chem. Biol. 14, 1323–1333 (2007).

    Article  CAS  Google Scholar 

  24. Fleckner, J. et al. Differential regulation of the human, interferon inducible tryptophanyl-tRNA synthetase by various cytokines in cell lines. Cytokine 7, 70–77 (1995).

    Article  CAS  Google Scholar 

  25. Kapoor, M. et al. Evidence for annexin II-S100A10 complex and plasmin in mobilization of cytokine activity of human TrpRS. J. Biol. Chem. 283, 2070–2077 (2008).

    Article  CAS  Google Scholar 

  26. Tzima, E. et al. VE-cadherin links tRNA synthetase cytokine to anti-angiogenic function. J. Biol. Chem. 280, 2405–2408 (2005).

    Article  CAS  Google Scholar 

  27. Tzima, E. et al. Biologically active fragment of a human tRNA synthetase inhibits fluid shear stress-activated responses of endothelial cells. Proc. Natl. Acad. Sci. USA 100, 14903–14907 (2003).

    Article  CAS  Google Scholar 

  28. Dorrell, M.I. et al. Combination angiostatic therapy completely inhibits ocular and tumor angiogenesis. Proc. Natl. Acad. Sci. USA 104, 967–972 (2007).

    Article  CAS  Google Scholar 

  29. Nollet, F., Kools, P. & van Roy, F. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. J. Mol. Biol. 299, 551–572 (2000).

    Article  CAS  Google Scholar 

  30. Shapiro, L. et al. Structural basis of cell-cell adhesion by cadherins. Nature 374, 327–337 (1995).

    Article  CAS  Google Scholar 

  31. Patel, S.D. et al. Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell 124, 1255–1268 (2006).

    Article  CAS  Google Scholar 

  32. May, C. et al. Identification of a transiently exposed VE-cadherin epitope that allows for specific targeting of an antibody to the tumor neovasculature. Blood 105, 4337–4344 (2005).

    Article  CAS  Google Scholar 

  33. Yang, X.L. et al. Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase. Structure 15, 793–805 (2007).

    Article  CAS  Google Scholar 

  34. Yang, X.L. et al. Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains. Proc. Natl. Acad. Sci. USA 100, 15376–15380 (2003).

    Article  CAS  Google Scholar 

  35. Yu, Y. et al. Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment: insights into substrate recognition, tRNA binding, and angiogenesis activity. J. Biol. Chem. 279, 8378–8388 (2004).

    Article  CAS  Google Scholar 

  36. Zhou, Q., Kiosses, W.B., Liu, J. & Schimmel, P. Tumor endothelial cell tube formation model for determining anti-angiogenic activity of a tRNA synthetase cytokine. Methods 44, 190–195 (2008).

    Article  CAS  Google Scholar 

  37. Larkin, M.A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).

    Article  CAS  Google Scholar 

  38. Laskowski, R.A., Moss, D.S. & Thornton, J.M. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231, 1049–1067 (1993).

    Article  CAS  Google Scholar 

  39. Winter, M.C., Shasby, S.S., Ries, D.R. & Shasby, D.M. Histamine selectively interrupts VE-cadherin adhesion independently of capacitive calcium entry. Am. J. Physiol. Lung Cell. Mol. Physiol. 287, L816–L823 (2004).

    Article  CAS  Google Scholar 

  40. Wiseman, T., Williston, S., Brandts, J.F. & Lin, L.N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179, 131–137 (1989).

    Article  CAS  Google Scholar 

  41. Austin, J. & First, E.A. Potassium functionally replaces the second lysine of the KMSKS signature sequence in human tyrosyl-tRNA synthetase. J. Biol. Chem. 277, 20243–20248 (2002).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank L. Shapiro and B. Honig (Columbia University) for reviewing the manuscript and D.M. Shasby (University Iowa College of Medicine) for providing a plasmid encoding wild-type VE-cadherin-Fc. This work was supported by grants CA92577 from the US National Cancer Institute and GM 15539 and U54RR025204 from the US National Institutes of Health, and by a fellowship from the US National Foundation for Cancer Research.

Author information

Authors and Affiliations

Authors

Contributions

Q.Z., M.K., M.G., R.B., L.A.N., P.S. and X.-L.Y. designed the research; Q.Z., M.K., M.G., X.X., M.H., C.P., E.A., M.-H.D. and X.-L.Y. performed the research; Q.Z., M.K., M.G., R.B., W.B.K., P.S. and X.-L.Y. analyzed data; and Q.Z., M.K., M.G., P.S. and X.-L.Y. wrote the paper.

Corresponding author

Correspondence to Xiang-Lei Yang.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1 and 2 and Supplementary Data 1 and 2 (PDF 5293 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhou, Q., Kapoor, M., Guo, M. et al. Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality. Nat Struct Mol Biol 17, 57–61 (2010). https://doi.org/10.1038/nsmb.1706

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1706

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing