A critical base pair in k-turns that confers folding characteristics and correlates with biological function

Nature Communications

Volumn 5, Issue , 2014, Pages

  McPhee, Scott A ^a   Huang, Lin ^a   Lilley, David M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; MAGNESIUM ION; METAL ION; SMALL NUCLEAR RNA; ION;

BIOLOGICAL ANALYSIS; CRYSTALLOGRAPHY; METAL BINDING; PROTEIN; RNA;

ARCHAEOGLOBUS FULGIDUS; ARTICLE; ATOM; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ELECTROPHORETIC MOBILITY; HALOARCULA MARISMORTUI; HISTOGRAM; KINK TURN; LIGAND BINDING; NONHUMAN; PREDICTIVE VALUE; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; RIBOSWITCH; RNA CONFORMATION; RNA FOLDING; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; BASE PAIRING; CHEMICAL STRUCTURE; CONFORMATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; FLUORESCENCE RESONANCE ENERGY TRANSFER; IONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION;

EID: 84923279873     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6127     Document Type: Article

References (38)

1. Klein, D. J., Schmeing, T. M., Moore, P. B. & Steitz, T. A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20, 4214-4221 (2001).
2. Vidovic, I., Nottrott, S., Hartmuth, K., Luhrmann, R. & Ficner, R. Crystal structure of the spliceosomal 15.5 kD protein bound to a U4 snRNA fragment. Molec. Cell 6, 1331-1342 (2000).
3. Moore, T., Zhang, Y., Fenley, M. O. & Li, H. Molecular basis of box C/D RNA-protein Interactions; Cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 12, 807-818 (2004).
4. Hamma, T. & Ferré-D'Amaré, A. R. Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 Å resolution. Structure 12, 893-903 (2004).
5. Li, L. & Ye, K. Crystal structure of an H/ACA box ribonucleoprotein particle. Nature 443, 302-307 (2006).
6. Montange, R. K. & Batey, R. T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441, 1172-1175 (2006).
7. Lescoute, A., Leontis, N. B., Massire, C. & Westhof, E. Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acids Res. 33, 2395-2409 (2005).
8. Liu, J. & Lilley, D. M. J. The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA. RNA 13, 200-210 (2007).
9. Daldrop, P. & Lilley, D. M. J. The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment. RNA 19, 357-364 (2013).
10. Goody, T. A., Melcher, S. E., Norman, D. G. & Lilley, D. M. J. The kink-turn motif in RNA is dimorphic, and metal ion dependent. RNA 10, 254-264 (2004).
11. Schroeder, K. T., Daldrop, P. & Lilley, D. M. J. RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn. Structure 19, 1233-1240 (2011).
12. Turner, B., Melcher, S. E., Wilson, T. J., Norman, D. G. & Lilley, D. M. J. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. RNA 11, 1192-1200 (2005).
13. Turner, B. & Lilley, D. M. J. The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA. J. Molec. Biol. 381, 431-442 (2008).
14. Wang, J. et al. Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein. Biophys. J. 103, 2541-2548 (2012).
15. Koonin, E. V., Bork, P. & Sander, C. A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme? Nucleic Acids Res. 22, 2166-2167 (1994).
16. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905-920 (2000).
17. Nottrott, S. et al. Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5′ stem-loop of U4 snRNA. EMBO J. 18, 6119-6133 (1999).
18. Kuhn, J. F., Tran, E. J. & Maxwell, E. S. Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res. 30, 931-941 (2002).
19. Watkins, N. J., Dickmanns, A. & Lührmann, R. Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol. Cell. Biol. 22, 8342-8352 (2002).
20. Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41, D226-D232 (2013).
21. Baird, N. J. & Ferre-D'Amare, A. R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19, 167-176 (2013).
22. Blouin, S. & Lafontaine, D. A. A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA 13, 1256-1267 (2007).
23. Peselis, A. & Serganov, A. Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch. Nat. Struct. Molec. Biol. 19, 1182-1184 (2012).
24. Huang, L. & Lilley, D. M. J. The molecular recognition of kink turn structure by the L7Ae class of proteins. RNA 19, 1703-1710 (2013).
25. Wang, J., Daldrop, P., Huang, L. & Lilley, D. M. J. The k-junction motif in RNA structure. Nucleic Acids Res. 42, 5322-5331 (2014).
26. Beaucage, S. L. & Caruthers, M. H. Deoxynucleoside phosphoramidites-a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22, 1859-1862 (1981).
27. Wilson, T. J., Zhao, Z.-Y., Maxwell, K., Kontogiannis, L. & Lilley, D. M. J. Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme. Biochemistry 40, 2291-2302 (2001).
28. Huang, L., Yin, P., Zhu, X., Zhang, Y. & Ye, K. Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100. Nucleic Acids Res. 39, 2954-2968 (2011).
29. Clegg, R. M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211, 353-388 (1992).
30. Karplus, P. A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030-1033 (2012).
31. Luo, Z., Rajashankar, K. & Dauter, Z. Weak data do not make a free lunch, only a cheap meal. Acta Crystallogr. D Biol. Crystallogr. 70, 253-260 (2014).
32. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
33. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
34. Keating, K. S. & Pyle, A. M. RCrane: semi-automated RNA model building. Acta Crystallogr. D Biol. Crystallogr. 68, 985-995 (2012).
35. Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355-367 (2011).
36. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235-242 (2011).
37. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
38. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21 (2010).