The plasticity of a structural motif in RNA: Structural polymorphism of a kink turn as a function of its environment

RNA

Volumn 19, Issue 3, 2013, Pages 357-364

  Daldrop, Peter ^a   Lilley, David M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

K turn; RNA structure; RNA protein interaction; SAM I riboswitch

Indexed keywords

ARTICLE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN MOTIF; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE;

BASE PAIRING; HALOARCULA MARISMORTUI; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA; RNA, ARCHAEAL;

EID: 84874305186     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.036657.112     Document Type: Article

References (28)

1. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, et al. 2010. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallog 66: 213-221.
2. Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR. 2012. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA 18: 759-770.
3. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920. (Pubitemid 30659939)
4. Blouin S, Lafontaine DA. 2007. 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. (Pubitemid 47080471)
5. Chao JA, Williamson Jr. 2004. Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Structure 12: 1165-1176. (Pubitemid 38900759)
6. DeLano WL. 2002. The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA. Goody TA, Melcher SE, Norman DG, Lilley DMJ. 2004. The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA 10: 254-264.
7. Hamma T, Ferré-D'Amaré AR. 2004. 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. (Pubitemid 38595777)
8. Heppell B, Lafontaine DA. 2008. Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot. Biochemistry 47: 1490-1499. (Pubitemid 351231200)
9. Klein DJ, Schmeing TM, Moore PB, Steitz TA. 2001. The kink-turn: A new RNA secondary structure motif. EMBO J 20: 4214-4221. (Pubitemid 32751837)
10. Lescoute A, Leontis NB, Massire C, Westhof E. 2005. Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acids Res 33: 2395-2409. (Pubitemid 41511259)
11. Liu J, Lilley DMJ. 2007. The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA. RNA 13: 200-210. (Pubitemid 46147896)
12. Mao H, White SA, Williamson Jr. 1999. A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nat Struct Biol 6: 1139-1147.
13. Matsumura S, Ikawa Y, Inoue T. 2003. Biochemical characterization of the kink-turn RNA motif. Nucleic Acids Res 31: 5544-5551. (Pubitemid 37441924)
14. Montange RK, Batey RT. 2006. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441: 1172-1175. (Pubitemid 43990740)
15. Montange RK, Mondragon E, van Tyne D, Garst AD, Ceres P, Batey RT. 2010. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol 396: 761-772.
16. Moore T, Zhang Y, Fenley MO, Li H. 2004. Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 12: 807-818. (Pubitemid 38595769)
17. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci 98: 4899-4903. (Pubitemid 32397054)
18. Schroeder KT, Lilley DMJ. 2009. Ion-induced folding of a kink turn that departs from the conventional sequence. Nucleic Acids Res 37: 7281-7289.
19. Schroeder KT, McPhee SA, Ouellet J, Lilley DMJ. 2010. A structural database for k-turn motifs in RNA. RNA 16: 1463-1468.
20. Schroeder KT, Daldrop P, Lilley DMJ. 2011. RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn. Structure 19: 1233-1240.
21. Schroeder KT, Daldrop P, McPhee SA, Lilley DMJ. 2012. Structure and folding of a rare, natural kink turn in RNA with an A.A pair at the 2b.2n position. RNA 18: 1257-1266.
22. Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. 2009. Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16: 1218-1223.
23. Turner B, Melcher SE, Wilson TJ, Norman DG, Lilley DMJ. 2005. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. RNA 11: 1192-1200. (Pubitemid 41132391)
24. Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, Long F, Murshudov GN. 2004. REFMAC5 dictionary: Organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr 60: 2184-2195. (Pubitemid 41742770)
25. Vidovic I, Nottrott S, Hartmuth K, Luhrmann R, Ficner R. 2000. Crystal structure of the spliceosomal 15.5 kD protein bound to a U4 snRNA fragment. Mol Cell 6: 1331-1342. (Pubitemid 32045926)
26. White SA, Hoeger M, Schweppe JJ, Shillingford A, Shipilov V, Zarutskie J. 2004. Internal loop mutations in the ribosomal protein L30 binding site of the yeast L30 RNA transcript. RNA 10: 369-377. (Pubitemid 38240997)
27. Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.
28. Wozniak AK, Nottrott S, Kuhn-Holsken E, Schroder GF, Grubmuller H, Luhrmann R, Seidel CA, Oesterhelt F. 2005. Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements. RNA 11: 1545-1554. (Pubitemid 41396924)