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Solution structure and metal ion binding sites of the human CPEB3 ribozyme’s P4 domain

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Abstract

Three ribozymes are known to occur in humans, the CPEB3 ribozyme, the CoTC ribozyme, and the hammerhead ribozyme. Here, we present the NMR solution structure of a well-conserved motif within the CPEB3 ribozyme, the P4 domain. In addition, we discuss the binding sites and impact of Mg2+ and [Co(NH3)6]3+, a spectroscopic probe for [Mg(H2O)6]2+, on the structure. The well-defined P4 region is a hairpin closed with a UGGU tetraloop that shows a distinct electrostatic surface potential and a characteristic, strongly curved backbone trajectory. The P4 hairpin contains two specific Mg2+ binding sites: one outer-sphere binding site close to the proposed CPEB3 ribozyme active site with potential relevance for maintaining a compact fold of the ribozyme core, and one inner-sphere binding site, probably stabilizing the tetraloop structure. The structure of the tetraloop resembles an RNase III recognition structure, as previously described for an AGUU tetraloop. The detailed knowledge of the P4 domain and its metal ion binding preferences thus brings us closer to understanding the importance of Mg2+ binding for the CPEB3 ribozyme’s fold and function in the cell.

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References

  1. Luptak A, Szostak JW (2007) In: Lilley DMJ, Eckstein F (eds) Mammalian self-cleaving ribozymes. Royal Society of Chemistry, Cambridge, pp 123–133

    Google Scholar 

  2. Sigel A, Sigel H, Sigel RKO (eds) (2011) Structural and catalytic roles of metal ions in RNA. Metal ions in life sciences, vol 9. Royal Society of Chemistry, Cambridge

    Google Scholar 

  3. Hammann C, Hartmann RK, Marchfelder A (2007) Biol Chem 388:659–660

    Article  CAS  PubMed  Google Scholar 

  4. Teixeira A, Tahiri-Alaoui A, West S, Thomas B, Ramadass A, Martianov I, Dye M, James W, Proudfoot NJ, Akoulitchev A (2004) Nature 432:526–530

    Article  CAS  PubMed  Google Scholar 

  5. Martick M, Horan LH, Noller HF, Scott WG (2008) Nature 454:899–902

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. de la Pena M, Garcia-Robles I (2010) EMBO Rep 11:711–716

    Article  PubMed Central  PubMed  Google Scholar 

  7. Salehi-Ashtiani K, Luptak A, Litovchick A, Szostak JW (2006) Science 313:1788–1792

    Article  CAS  PubMed  Google Scholar 

  8. Talini G, Branciamore S, Gallori E (2011) Biochimie 93:1998–2005

    Article  CAS  PubMed  Google Scholar 

  9. Chadalavada DM, Gratton EA, Bevilacqua PC (2010) Biochemistry 49:5321–5330

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Webb CHT, Luptak A (2011) RNA Biol 8:719–727

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Gong B, Chen JH, Chase E, Chadalavada DM, Yajima R, Golden BL, Bevilacqua PC, Carey PR (2007) J Am Chem Soc 129:13335–13342

    Article  CAS  PubMed  Google Scholar 

  12. Nakano S-I, Proctor DJ, Bevilacqua PC (2001) Biochemistry 40:12022–12038

    Article  CAS  PubMed  Google Scholar 

  13. Veeraraghavan N, Ganguly A, Golden BL, Bevilacqua PC, Hammes-Schiffer S (2011) J Phys Chem B 115:8346–8357

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Chen J-H, Yajima R, Chadalavada DM, Chase E, Bevilacqua PC, Golden BL (2010) Biochemistry 49:6508–6518

    Article  CAS  PubMed  Google Scholar 

  15. Vogler C, Spalek K, Aerni A, Demougin P, Muller A, Huynh KD, Papassotiropoulos A, de Quervain DJ (2009) Front Behav Neurosci 3:4

    Article  PubMed Central  PubMed  Google Scholar 

  16. Cheong C, Cheong H-K (2010) In: Encyclopedia of life sciences. Wiley, Chichester. doi:10.1002/9780470015902.a0003135.pub2

  17. Deng NJ, Cieplak P (2010) Biophys J 98:627–636

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Korth MMT, Sigel RKO (2012) Chem Biodiv 9:2035–2049

    Article  CAS  Google Scholar 

  19. Sigel RKO, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM (2004) Nat Struct Biol 11:187–192

    Article  CAS  Google Scholar 

  20. Nozinovic S, Furtig B, Jonker HRA, Richter C, Schwalbe H (2010) Nucleic Acids Res 38:683–694

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Donghi D, Pechlaner M, Finazzo C, Knobloch B, Sigel RKO (2013) Nucleic Acids Res 41:2489–2504

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Fürtig B, Richter C, Bermel W, Schwalbe H (2004) J Biomol NMR 28:69–79

    Article  PubMed  Google Scholar 

  23. Banas P, Hollas D, Zgarbova M, Jurecka P, Orozco M, Cheatham TE, Sponer J, Otyepka M (2010) J Chem Theor Comput 6:3836–3849

    Article  CAS  Google Scholar 

  24. Chanfreau C, Buckle M, Jacquier A (2000) Proc Natl Acad Sci USA 97:3142–3147

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Seipelt RL, Zheng BH, Asuru A, Rymond BC (1999) Nucleic Acids Res 27:587–595

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Wu HH, Yang PK, Butcher SE, Kang S, Chanfreau G, Feigon J (2001) EMBO J 20:7240–7249

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Ghazal G, Ge DL, Gervais-Bird J, Gagnon J, Abou Elela S (2005) Mol Cell Biol 25:2981–2994

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  28. Freisinger E, Sigel RKO (2007) Coord Chem Rev 251:1834–1851

    Article  CAS  Google Scholar 

  29. Erat MC, Sigel RKO (2011) Met Ions Life Sci 9:37–100

    Google Scholar 

  30. Sigel RKO, Pyle AM (2007) Chem Rev 107:97–113

    Article  CAS  PubMed  Google Scholar 

  31. Schnabl J, Sigel RKO (2010) Curr Opin Chem Biol 14:269–275

    Article  CAS  PubMed  Google Scholar 

  32. Sreedhara A, Cowan JA (2002) Biometals 15:211–223

    Article  CAS  PubMed  Google Scholar 

  33. Ennifar E, Walter P, Dumas P (2003) Nucleic Acids Res 31:2671–2682

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Petrov AS, Pack GR, Lamm G (2004) J Phys Chem B 108:6072–6081

    Article  CAS  Google Scholar 

  35. Sigel RKO, Sigel H (2013) In: Pecoraro VL (ed) Bioinorganic fundamentals and applications: metals in natural living systems and metals in toxicology and medicine. Comprehensive inorganic chemistry II, vol 3. Elsevier, Amsterdam, pp 623–660

    Google Scholar 

  36. Cowan JA (1993) J Inorg Biochem 49:171–175

    Article  CAS  PubMed  Google Scholar 

  37. Rowinska-Zyrek M, Skilandat M, Sigel RKO (2013) Z Anorg Allg Chem 639:1313–1320

    Article  CAS  Google Scholar 

  38. Schmitz M (2004) Nucleic Acids Res 32:6358–6366

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  39. Gallo S, Furler M, Sigel RKO (2005) Chimia 59:812–816

    Article  CAS  Google Scholar 

  40. Kao C, Rüdisser S, Zheng M (2001) Methods 23:201–205

    Article  CAS  PubMed  Google Scholar 

  41. Glasoe PK, Long FA (1960) J Phys Chem 64:188–190

    Article  CAS  Google Scholar 

  42. Donghi D, Johannsen S, Sigel RKO, Freisinger E (2012) Chimia 66:791–797

    Article  CAS  PubMed  Google Scholar 

  43. Güntert P, Mumenthaler C, Wüthrich K (1997) J Mol Biol 273:283–298

    Article  PubMed  Google Scholar 

  44. Brünger AT (1992) X-PLOR. Version 3.1. A system for X-ray crystallography and NMR. Yale University Press, New Haven

    Google Scholar 

  45. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Acta Crystallogr D 54:905–921

    Article  PubMed  Google Scholar 

  46. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) J Magn Reson 160:65–73

    Article  CAS  PubMed  Google Scholar 

  47. Schwieters CD, Kuszewski JJ, Clore GM (2006) Prog Nucl Magn Reson Spectrosc 48:47–62

    Article  CAS  Google Scholar 

  48. Koradi R, Billeter M, Wüthrich K (1996) J Mol Graph Model 14:29–32, 51–55

    Google Scholar 

  49. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Proc Natl Acad Sci USA 98:10037–10041

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  50. Sigel H (2004) Pure Appl Chem 76:1869–1886

    CAS  Google Scholar 

  51. Varani G, Aboulela F, Allain FHT (1996) Prog Nucl Magn Reson Spectrosc 29:51–127

    Article  CAS  Google Scholar 

  52. Allain FHT, Varani G (1995) J Mol Biol 250:333–353

    Article  CAS  PubMed  Google Scholar 

  53. Jucker FM, Heus HA, Yip PF, Moors EHM, Pardi A (1996) J Mol Biol 264:968–980

    Article  CAS  PubMed  Google Scholar 

  54. Woodson SA (2005) Curr Opin Chem Biol 9:104–109

    Article  CAS  PubMed  Google Scholar 

  55. Pechlaner M, Sigel RKO (2012) Met Ions Life Sci 10:1–42

    Google Scholar 

  56. Sigel H, Bianchi EM, Corfù NA, Kinjo Y, Tribolet R, Martin RB (2001) Chem Eur J 7:3729–3737

    Article  CAS  PubMed  Google Scholar 

  57. Sigel H, Griesser R (2005) Chem Soc Rev 34:875–900

    Article  CAS  PubMed  Google Scholar 

  58. Erat MC, Sigel RKO (2007) Inorg Chem 46:11224–11234

    Article  CAS  PubMed  Google Scholar 

  59. Rüdisser S, Tinoco I (2000) J Mol Biol 295:1211–1223

    Article  PubMed  Google Scholar 

  60. Lebars I, Lamontagne B, Yoshizawa S, Elela SA, Fourmy D (2001) EMBO J 20:7250–7258

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  61. Wu H, Henras A, Chanfreau G, Feigon J (2004) Proc Natl Acad Sci USA 101:8307–8312

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  62. Girard FC, Ottink OM, Ampt KAM, Tessari M, Wijmenga SS (2007) Nucleic Acids Res 35:2800–2811

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  63. Nassal M, Schaller H (1996) J Viral Hepatitis 3:217–226

    Article  CAS  Google Scholar 

  64. Ke A, Zhou K, Ding F, Cate JHD, Doudna JA (2004) Nature 429:201–205

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

Financial support from a Sciex postdoctoral grant (no. 11.156, to M.R.-Z.), a Marie Curie fellowship (no. PIEF-GA-2012-329700 to M.R.-Z.), the Swiss National Science Foundation (to R.K.O.S.), and the University of Zurich is gratefully acknowledged. R.K.O.S. is a recipient of a European Research Council Starting Grant (microRNA). Structure coordinates have been deposited in the RCSB Protein Data Bank (ID 2M5U), and chemical shifts have been deposited in the Biological Magnetic Resonance Bank with accession code 19081.

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Authors and Affiliations

  1. Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland

    Miriam Skilandat, Magdalena Rowinska-Zyrek & Roland K. O. Sigel

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  1. Miriam Skilandat
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  2. Magdalena Rowinska-Zyrek
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  3. Roland K. O. Sigel
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Correspondence to Roland K. O. Sigel.

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M. Skilandat and M. Rowinska-Zyrek contributed equally to this work.

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Skilandat, M., Rowinska-Zyrek, M. & Sigel, R.K.O. Solution structure and metal ion binding sites of the human CPEB3 ribozyme’s P4 domain. J Biol Inorg Chem 19, 903–912 (2014). https://doi.org/10.1007/s00775-014-1125-6

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