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High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove

Nature Structural & Molecular Biology volume 26, pages 1114–1122 (2019)Cite this article

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Abstract

T-box riboswitches are modular bacterial noncoding RNAs that sense and regulate amino acid availability through direct interactions with tRNAs. Between the 5′ anticodon-binding stem I domain and the 3′ amino acid sensing domains of most T-boxes lies the stem II domain of unknown structure and function. Here, we report a 2.8-Å cocrystal structure of the Nocardia farcinica ileS T-box in complex with its cognate tRNAIle. The structure reveals a perpendicularly arranged ultrashort stem I containing a K-turn and an elongated stem II bearing an S-turn. Both stems rest against a compact pseudoknot, dock via an extended ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA. Contrary to proposed distal contacts to the tRNA elbow region, stem II locally reinforces the codon-anticodon interactions between stem I and tRNA, achieving low-nanomolar affinity. This study illustrates how mRNA junctions can create specific binding sites for interacting RNAs of prescribed sequence and structure.

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Fig. 1: Overall structure of the N. farcinica ileS T-box in complex with tRNAIle.
Fig. 2: Recognition of tRNA anticodon by the ileS T-box riboswitch.
Fig. 3: Stabilization of specifier-anticodon interaction by the S-turn motif.
Fig. 4: tRNA recognition by the T-box anticodon-binding groove.
Fig. 5: Stem IIA/B forms a compact pseudoknot to position stems I and II.
Fig. 6: Structural comparison with T-boxes containing canonical long stem I.

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Data availability

Atomic coordinates and structure factor amplitudes for the RNA have been deposited at the Protein Data Bank under accession code PDB 6UFM. Source data for Figs. 2d, 3e and 5d are available online. All other data generated or analyzed during this study are included in this published article or available upon request.

References

  1. Zhang, J. & Ferre-D’Amare, A. R. Structure and mechanism of the T-box riboswitches. Wiley Interdiscip. Rev. RNA 6, 419–433 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Grundy, F. J. & Henkin, T. M. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 74, 475–482 (1993).

    CAS  PubMed  Google Scholar 

  3. Suddala, K. C. & Zhang, J. An evolving tale of two interacting RNAs-themes and variations of the T-box riboswitch mechanism. IUBMB Life 71, 1167–1180 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Vitreschak, A. G., Mironov, A. A., Lyubetsky, V. A. & Gelfand, M. S. Comparative genomic analysis of T-box regulatory systems in bacteria. RNA 14, 717–735 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Gutierrez-Preciado, A., Henkin, T. M., Grundy, F. J., Yanofsky, C. & Merino, E. Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol. Mol. Biol. Rev. 73, 36–61 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Sherwood, A. V., Grundy, F. J. & Henkin, T. M. T box riboswitches in Actinobacteria: translational regulation via novel tRNA interactions. Proc. Natl Acad. Sci. USA 112, 1113–1118 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Frohlich, K. M. et al. Discovery of small molecule antibiotics against a unique tRNA-mediated regulation of transcription in Gram-positive bacteria. ChemMedChem 4, 758–769 (2019).

    Google Scholar 

  8. Grigg, J. C. & Ke, A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 21, 2025–2032 (2013).

    CAS  PubMed  Google Scholar 

  9. Zhang, J. & Ferré-D’Amaré, A. R. Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363–366 (2013).

    Article  CAS  PubMed  Google Scholar 

  10. Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065–1077 (2006).

    CAS  PubMed  Google Scholar 

  11. Reiter, N. J. et al. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 468, 784–789 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Lehmann, J., Jossinet, F. & Gautheret, D. A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNase P and T-box leaders. Nucleic Acids Res. 41, 5494–5502 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Suddala, K. C. et al. Hierarchical mechanism of amino acid sensing by the T-box riboswitch. Nat. Commun. 9, 1896 (2018).

    PubMed  PubMed Central  Google Scholar 

  14. Zhang, J. et al. Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand. eLife 7, e39518 (2018).

    PubMed  PubMed Central  Google Scholar 

  15. Sherwood, A. V., Frandsen, J. K., Grundy, F. J. & Henkin, T. M. New tRNA contacts facilitate ligand binding in a Mycobacterium smegmatis T box riboswitch. Proc. Natl Acad. Sci. USA 115, 3894–3899 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Lilley, D. M. The K-turn motif in riboswitches and other RNA species. Biochim. Biophys. Acta 1839, 995–1004 (2014).

    CAS  PubMed  Google Scholar 

  17. Zhang, J. & Ferré-D’Amaré, A. R. Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Mol. Cell 55, 148–155 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Rollins, S. M., Grundy, F. J. & Henkin, T. M. Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Mol. Microbiol. 25, 411–421 (1997).

    CAS  PubMed  Google Scholar 

  19. Correll, C. C., Freeborn, B., Moore, P. B. & Steitz, T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91, 705–712 (1997).

    CAS  PubMed  Google Scholar 

  20. Yang, X., Gérczei, T., Glover, L. & Correll, C. C. Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nat. Struct. Biol. 8, 968–973 (2001).

    CAS  PubMed  Google Scholar 

  21. Grosjean, H. & Westhof, E. An integrated, structure- and energy-based view of the genetic code. Nucleic Acids Res. 44, 8020–8040 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Caserta, E., Liu, L. C., Grundy, F. J. & Henkin, T. M. Codon-anticodon recognition in the Bacillus subtilis glyQS T box riboswitch: RNA-dependent codon selection outside the ribosome. J Biol Chem. 290, 23336–23347 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Winkler, W. C., Grundy, F. J., Murphy, B. A. & Henkin, T. M. The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA 7, 1165–1172 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Leontis, N. B., Stombaugh, J. & Westhof, E. Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84, 961–973 (2002).

    CAS  PubMed  Google Scholar 

  25. Suslov, N. B. et al. Crystal structure of the Varkud satellite ribozyme. Nat. Chem. Biol. 11, 840–846 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Gabdulkhakov, A., Nikonov, S. & Garber, M. Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Acta Crystallogr. D Biol. Crystallogr. 69, 997–1004 (2013).

    CAS  PubMed  Google Scholar 

  27. Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R. & Patel, D. J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167–1171 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Edwards, T. E. & Ferré-D’Amaré, A. R. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14, 1459–1468 (2006).

    CAS  PubMed  Google Scholar 

  29. Gilbert, S. D., Rambo, R. P., Van Tyne, D. & Batey, R. T. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat. Struct. Mol. Biol. 15, 177–182 (2008).

    CAS  PubMed  Google Scholar 

  30. Klein, D. J., Edwards, T. E. & Ferre-D’Amare, A. R. Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat. Struct. Mol. Biol. 16, 343–344 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Cate, J. H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696–1699 (1996).

    CAS  PubMed  Google Scholar 

  32. Westhof, E. & Fritsch, V. RNA folding: beyond Watson-Crick pairs. Structure 8, R55–R65 (2000).

    CAS  PubMed  Google Scholar 

  33. Leontis, N. B. & Westhof, E. A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J. Mol. Biol. 283, 571–583 (1998).

    CAS  PubMed  Google Scholar 

  34. Kreuzer, K. D. & Henkin, T. M. The T-box riboswitch: tRNA as an effector to modulate gene regulation. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.RWR-0028-2018 (2018).

  35. Demeshkina, N., Jenner, L., Westhof, E., Yusupov, M. & Yusupova, G. A new understanding of the decoding principle on the ribosome. Nature 484, 256–259 (2012).

    CAS  PubMed  Google Scholar 

  36. Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065–1077 (2006).

    CAS  PubMed  Google Scholar 

  37. Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001).

    CAS  PubMed  Google Scholar 

  38. Hood, I. V. et al. Crystal structure of an adenovirus virus-associated RNA. Nat. Commun. 10, 2871 (2019).

    PubMed  PubMed Central  Google Scholar 

  39. Taufer, M. et al. PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Res. 37, D127–D135 (2009).

    CAS  PubMed  Google Scholar 

  40. Wickiser, J. K., Winkler, W. C., Breaker, R. R. & Crothers, D. M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18, 49–60 (2005).

    CAS  PubMed  Google Scholar 

  41. Zhang, J., Lau, M. W. & Ferre-D’Amare, A. R. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 49, 9123–9131 (2010).

    CAS  PubMed  Google Scholar 

  42. Santner, T., Rieder, U., Kreutz, C. & Micura, R. Pseudoknot preorganization of the preQ1 class I riboswitch. J. Am. Chem. Soc. 134, 11928–11931 (2012).

    CAS  PubMed  Google Scholar 

  43. Lemay, J. F. et al. Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet. 7, e1001278 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Suddala, K. C. et al. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res. 41, 10462–10475 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Day, E. S., Cote, S. M. & Whitty, A. Binding efficiency of protein-protein complexes. Biochemistry 51, 9124–9136 (2012).

    CAS  PubMed  Google Scholar 

  46. Van Treeck, B. & Parker, R. Emerging roles for intermolecular RNA-RNA interactions in RNP assemblies. Cell 174, 791–802 (2018).

    PubMed  PubMed Central  Google Scholar 

  47. Jain, A. & Vale, R. D. RNA phase transitions in repeat expansion disorders. Nature 546, 243–247 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Leontis, N. B. & Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Zhao, H., Piszczek, G. & Schuck, P. SEDPHAT-a platform for global ITC analysis and global multi-method analysis of molecular interactions. Methods 76, 137–148 (2015).

    CAS  PubMed  Google Scholar 

  50. Adams, P. & Al, E. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D 66, 213–221 (2010).

    CAS  Google Scholar 

  51. McCoy, A. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007).

    CAS  Google Scholar 

  52. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Chou, F. C., Sripakdeevong, P., Dibrov, S. M., Hermann, T. & Das, R. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat. Methods 10, 74–76 (2013).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank I. Botos for computational support, G. Piszczek and D. Wu for support in biophysical analyses, F. Dyda for suggesting the use of zero-dose correction, and S. Li, C. Bou-Nader, J.M. Gordon, C. Stathopoulos, and A. Ferré-D’Amaré for discussions. Data were collected at Southeast Regional Collaborative Access Team (SER-CAT) 22-ID beamline at the Advanced Photon Source of the Argonne National Laboratory, supported by the US Department of Energy under Contract No. W-31–109-Eng-38. This work was supported by the intramural research program of NIDDK, NIH, an NIH Deputy Director for Intramural Research (DDIR) Innovation Award and a DDIR Challenge Award to J.Z.

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Authors and Affiliations

  1. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA

    Krishna C. Suddala & Jinwei Zhang

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  1. Krishna C. Suddala
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Contributions

K.C.S. and J.Z. conceived the study and designed crystallization constructs. K.C.S. prepared the RNA and crystal samples, collected diffraction data, and performed all biochemical analyses. K.C.S. and J.Z determined and refined the structure, prepared figures and wrote the paper.

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Correspondence to Jinwei Zhang.

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Peer review information Anke Sparmann was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Binding of tRNAIle by the N. farcinica ileS T-box riboswitch and effect of agarose on crystal morphology.

a, Electrophoretic mobility shift assay (EMSA) using 10% non-denaturing polyacrylamide gel showing binding of T-box length variants to tRNAIle. T-box1–29 (stem I) bands were poorly stained by GelRed and are indicated by the dashed box. b, EMSA titration showing the binding of tRNAIle by N. farcinica ileS T-box1–98. Lanes 1–5 (left to right): 0:1, 1:0, 1:0.5, 1:1 and 1:2 mixing ratios of T-box1–98:tRNAIle. 10 μM of T-box1–98 was used for the assay. c, Crystals grown in the absence of agarose appear as thin plates with parasitic growth from the corners. Crystals were grown at 21 °C by vapor diffusion by mixing an equal volume of reservoir solution containing 20% PEG 3350, 0.1 M Bis-Tris (HCl), pH 6.5 and 200 mM Li2SO4. d, Crystals grown under similar conditions as in c but in the presence of ~0.1 % low-melting-point agarose. In the presence of agarose, crystals grew as thick rectangular prisms with sharp edges and exhibited improved diffraction properties. Scale bar, ~100 μm.

Extended Data Fig. 2 Isothermal titration calorimetry (ITC) analysis of tRNAIle binding by the ileS T-box riboswitch length variants.

a−d, Representative ITC isotherms for N. farcinica WT RNAIle binding to (a) T-box1–98, (b) T-box1–89, (c) T-box1–77, and (d) T-box1–29. e, ITC isotherm of tRNAIle anticodon stem loop (ASL) binding to T-box1–98 (WT). f,g, ITC isotherms for N. farcinica WT RNAIle binding to (f) T-box1–99 (with an extra 3′-G), and (g) T-box1–89 A84C mutant. h,i, ITC isotherms of (h) tRNAIle G19C mutant and (i) M. smegmatis tRNAIle binding to T-box1–98 (WT). The construct names and the Kd values (mean ± s.d., n = 4 for a,e; n = 3 for b,d,f; n = 2 for c,g−i) are reported in the top and bottom panels of the ITC isotherms.

Extended Data Fig. 3 ITC analysis of the effects of single nucleobase substitutions on the ileS T-box and tRNAIle.

a−d, Representative ITC isotherms for WT tRNAIle binding by T-box1–98 stem I mutants (a) A8G, (b) A16U, (c) A16G, (d) U17A, (d) C18G. e, T-box1–98 binding to tRNAIle tA35G mutant. f,g, ITC isotherms for WT tRNAIle binding by T-box1–98 stem I mutants (f) C18G and (g) C18U. h, T-box1–98 U17A mutant binding to tRNAIle tA35U mutant. i, ITC isotherms for WT tRNAIle binding by T-box1–98 stem I mutant A19U. j−s, tRNAIle binding to T-box1–98 stem II mutants (j) G37U, (k) A38U, (l) A39U, (m) A66U, (n) G67U, (o) A69U, (p) G70U, (q) A71U, (r) G85C and (s) U90C. t, Sequence and secondary structure of T-box1–98 for reference. The construct names and the Kd values (mean ± s.d., n = 3 for a, f, h, n, o, q, s; n = 2 for b−e, g, i−m, p, r) are reported in the top and bottom panels of the ITC isotherms.

Extended Data Fig. 4 Representative X-ray crystallographic electron density maps.

a, Composite simulated anneal-omit 2Fo – Fc electron density calculated using the final model (1.0 s.d.) superimposed with the final refined model. b,c, Portions of the map showing the tRNA anticodon−T-box specifier duplex region (b) and the characteristic S-like backbone bend of the stem II S turn (c).

Extended Data Fig. 5 Similarity between ileS T-box stem I distal loop and tRNAIle anticodon stem loop (ASL).

Superposition of the ileS stem I distal loop (orange) with tRNAIle ASL (green) showing structural similarities.

Extended Data Fig. 6 Comparison of S-turn structures and S-turn-mediated RNA-RNA interactions.

a−d, The S-turn (or loop E) motif from (a) N. farcinica ileS T-box riboswitch structure, (b) glyQ T-box stem I from Oceanobacillus iheyensis (PDB 4LCK)9 (c) 23S rRNA from the Haloarcula marismortui large ribosomal subunit (PDB 4V9F)26, and (d) glutamine riboswitch (PDB 5DDP). e, Overlay of the S-turn structures in a−d. f, Stabilization of codon-anticodon helix by the stem II S-turn in ileS T-box riboswitch. g, Interactions between an S turn and a neighboring helix in 23S rRNA from H. marismortui. h, Interactions between an atypical S-turn motif in helix 6 of the Varkud satellite (VS) ribozyme (PDB 4R4V)25 and A652 of helix 2. Red and green dashes represent H-bonds involving nucleotides in the backbone-turn-containing strand and the opposite strand, respectively.

Extended Data Fig. 7 Examples of the recurring inclined tandem A-minor (ITAM) motifs in RNA structures.

a, The inclined tandem A-minor (ITAM) motif observed in the ileS T-box−tRNAIle structure. b−d, Similar ITAM motifs observed in the (b) TPP riboswitch (PDB 2GDI)27, (c) SAM-II riboswitch (PDB 2QWY)29 and (d) preQ1-I riboswitch (PDB 3FU2)30 crystal structures. For comparison, the motifs shown in b−d are formed by adjacent adenosines on the same strand, whereas the ITAM motif in a uses cross-strand stacked adenosines from opposite strands. This configuration allows both the ribose and the nucleobases from both adenosines to contact the C-G base pair. The inclined adenosine motif in c is unusual in that three adjacent, stacked adenosines span the width of a single C-G base pair and form multiple contacts with it. The motif in d (also termed the A-amino kissing motif) involves the Watson−Crick edges of the adenosines and does not involve interactions with the ribose. These interactions are formed by L3 loop adenosines of the preQ1-I riboswitch and are common in many other H-type pseudoknots.

Extended Data Fig. 8 Three different strategies to stabilize the codon−anticodon duplex.

a, The minor groove side of the N. farcinica ileS T-box stem II S turn interacts extensively with the minor groove of the anticodon-specifier duplex. In particular, the A38-A69 inclined tandem A-minor (ITAM) motif stabilizes the C18-tG34 base pair. G70 and A71 stack with the top layer of the S turn (G37•A69) and stabilize the U17-tA35 and A16-tU36 pairs, respectively (Fig. 3d). b, The conserved A1492 and A1493 of ribosomal RNA in the ribosome A site interact with the codon−anticodon duplex via tandem, stacked A-minor interactions (similar to G70 and A71 in a) in conjunction with the G530 latch (similar to A38 and A69 in a) to ensure decoding fidelity35,36,37. c, Similarly, in the adenovirus virus-associated RNA I (VA-I RNA), A36 stabilizes a 3-bp kissing pseudoknot formed between residues 103–105 in loop 8 (5′-ACC-3′, anticodon-like) and residues 124–126 (5′-GGU-3′, codon-like) of loop 10, through extensive A-minor interactions between A36 and the minor groove38.

Extended Data Fig. 9 Intermolecular interface of the N. farcinica T-box−tRNAIle complex.

a, Solvent-accessible surface colored according to area buried from light blue or white (no burial) to red (>125 Å2 per residue). b, Open-book view of the binding interface. c,d, Plots of solvent-accessible surface area buried per residue (Å2) on the tRNA (c) and T-box (d).

Extended Data Fig. 10 Structural model of a canonical, feature-complete T-box riboswitch stem I and II domains in complex with its cognate tRNA.

Model of a canonical, feature-complete T-box riboswitch, such as the originally described B. subtilis tyrS T-box containing a long stem I (salmon), stem II (blue) and stem IIA/B pseudoknot (cyan) elements bound to its cognate tRNA (green). The composite structural model is derived by combining the cocrystal structures of the ileS T-box riboswitch bound to tRNAIle and the cocrystal structure of the Oceanobacillus iheyensis glyQ T-box stem I bound to tRNAGly (PDB 4LCK)9. tRNAs from both structures were superimposed, as shown in Fig. 6b. The distal loop of the ultrashort stem I from the ileS T-box was then replaced with the long, canonical stem I from the glyQ T-box.

Supplementary information

Supplementary Information

Supplementary Table 1

Reporting Summary

Supplementary Video 1

360° view of the 2.82 -Å cocrystal structure of the N. farcinica ileS T-box in complex with tRNAIle.

Source data

Source Data Fig. 2

Statistical Source Data, for ITC analysis

Source Data Fig. 3

Statistical Source Data, for ITC analysis

Source Data Fig. 5

Statistical Source Data, for ITC analysis

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Suddala, K.C., Zhang, J. High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. Nat Struct Mol Biol 26, 1114–1122 (2019). https://doi.org/10.1038/s41594-019-0335-6

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