Kink-turn motif

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The kink-turn motif
A common RNA structural motif that consists of helix–internal loop–helix motif that introduces a very tight kink into the helical axis.


Contents

Introduction

 
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A C G U

The kink-turn motif is a common RNA structural motif that consists of helix–internal loop–helix motif that introduces a very tight kink into the helical axis, as illustrated in the figure below and 3D structure window on the right. Originally identified in the course of analyzing the large ribosomal subunit[1], this RNA structural motif was also identified in other RNAs. Particular instances have been called the GA motif [2].


The kink-turn motif includes the A-minor motif. Many kink-turns bind proteins; however, that trait is not universal. They can mediate RNA tertiary structure interactions as well.

An excellent introduction can be found here as part of a structural database for k-turn motifs in RNA by the Lilley group[3].

Kink-turns fall into two conformational classes, called N3 and N1. The classes differ in the pattern of hydrogen bonding in the core, and that pattern is determined by the basepair adjacent to the G•A pairs[4].


Structures Containing the Motif

 

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A C G U

  • The Large Ribosomal Subunit contains 9 identified kink-turns[1][3]: and Kt-7 ; and Kt-15 ; ; and Kt-42 ; and Kt-46 ); and Kt-58 ; and Kt-4/5 ; and Kt-94/99 with of 3cc2; as observed in 2wh2 (While present based on sequence comparison, Kt-78 is in a portion of the large subunit not visible in the crystal structure of 3cc2.)
  • observed in the solved structure of the Haloarcula large ribosomal subunit shows they are on the surface of the subunit: , , , , , , , and . (A ninth kink-turn, Kt-78, though present in Haloarcula marismortui rRNA is in a portion not resolved in the actual Haloarcula marismortui structure, yet is also on the surface.)
  • See all of the 23S rRNA kink-turns and others on this page in greater detail following the appropriate links on this page at a structural database for k-turn motifs in RNA by the Lilley group[3].
  • The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to the kink-turn of a U4 spliceosomal RNA fragment (1e7k)[5]. The fact both the box C/D small nucleolar RNAs and the spliceosomal U4 RNA share this motif, and in fact bind the same protein, was observed[6][5] even before the kink-turn was shown to be a widespread RNA motif.
  • The from Sulfolobus solfataricus has two kink-turns that are bound by L7Ae (3pla)[7]. .
  • A. fulgidus small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae (1rlg)[8].
  • Pyrococcus furiosus small ribonucleoprotein particle box H/ACA RNA (2hvy[9],3hax,3hay[10]) has a kink turn that is bound directly by L7ae in a complex of several proteins.
  • In the Pyrococcus furiosus small ribonucleoprotein particle structure a box C/D RNA has two kink-turns bound by L7Ae (3nvm, 3nvk, 3nvi, and 3nmu)[11].
  • L7Ae protein as a subunit of archaeal RNase P binds to two kink-turns in the Pyrococcus furiosus RNase P RNA[12], [13]
  • Azoarcus group I intron:
  • The Azoarcus group I intron (1u6b, 1zzn, 3bo2, 3bo3, 3bo4, and 3iin)[14][15][16][17] has a 'reverse' kink-turn. Overlay of the Azoarcus group I intron reverse kink-turn with a typical one (Kt-7) clearly illustrates the difference. PUT A SCENE HERE OF ALIGNMENT OF THIS WITH KT-7 with each Kt colored differently
  • highlighted within the solved structure of theAzoarcus group I intron.
  • S. cerevisiae L30e bound to its pre-mRNA (1t0k)[18] has a kink-turn with a protein bound.
  • S-adenosylmethionine riboswitch regulatory mRNA element from Thermoanaerobacter tengcongensis (2gis)[19] has a kink-turn.
  • The lysine riboswitch regulatory mRNA element from Thermotoga maritima (3dox) has a kink-turn
  • 1nkw – The Large Ribosomal Subunit From Deinococcus radiodurans[20]
  • The small ribosomal subunit (2wh1) has two kink-turns.

See Also

References

  1. 1.0 1.1 Klein DJ, Schmeing TM, Moore PB, Steitz TA. The kink-turn: a new RNA secondary structure motif. EMBO J. 2001 Aug 1;20(15):4214-21. PMID:11483524 doi:http://dx.doi.org/10.1093/emboj/20.15.4214
  2. Winkler WC, Grundy FJ, Murphy BA, Henkin TM. The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA. 2001 Aug;7(8):1165-72. PMID:11497434
  3. 3.0 3.1 3.2 Schroeder KT, McPhee SA, Ouellet J, Lilley DM. A structural database for k-turn motifs in RNA. RNA. 2010 Aug;16(8):1463-8. Epub 2010 Jun 18. PMID:20562215 doi:10.1261/rna.2207910
  4. Huang L, Wang J, Lilley DM. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function. Nucleic Acids Res. 2016 Mar 25. pii: gkw201. PMID:27016741 doi:http://dx.doi.org/10.1093/nar/gkw201
  5. 5.0 5.1 Vidovic I, Nottrott S, Hartmuth K, Luhrmann R, Ficner R. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol Cell. 2000 Dec;6(6):1331-42. PMID:11163207
  6. Watkins NJ, Segault V, Charpentier B, Nottrott S, Fabrizio P, Bachi A, Wilm M, Rosbash M, Branlant C, Luhrmann R. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell. 2000 Oct 27;103(3):457-66. PMID:11081632
  7. Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K. Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Nature. 2011 Jan 27;469(7331):559-563. PMID:21270896 doi:10.1038/nature09688
  8. Moore T, Zhang Y, Fenley MO, Li H. Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure. 2004 May;12(5):807-18. PMID:15130473 doi:http://dx.doi.org/10.1016/j.str.2004.02.033
  9. Li L, Ye K. Crystal structure of an H/ACA box ribonucleoprotein particle. Nature. 2006 Sep 21;443(7109):302-7. Epub 2006 Aug 30. PMID:16943774 doi:http://dx.doi.org/10.1038/nature05151
  10. Duan J, Li L, Lu J, Wang W, Ye K. Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. Mol Cell. 2009 May 14;34(4):427-39. PMID:19481523 doi:10.1016/j.molcel.2009.05.005
  11. Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H. Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Mol Cell. 2010 Sep 24;39(6):939-49. PMID:20864039 doi:10.1016/j.molcel.2010.08.022
  12. Lai SM, Lai LB, Foster MP, Gopalan V. The L7Ae protein binds to two kink-turns in the Pyrococcus furiosus RNase P RNA. Nucleic Acids Res. 2014 Dec 1;42(21):13328-38. doi: 10.1093/nar/gku994. Epub 2014, Oct 31. PMID:25361963 doi:http://dx.doi.org/10.1093/nar/gku994
  13. Cho IM, Lai LB, Susanti D, Mukhopadhyay B, Gopalan V. Ribosomal protein L7Ae is a subunit of archaeal RNase P. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14573-8. doi:, 10.1073/pnas.1005556107. Epub 2010 Jul 30. PMID:20675586 doi:http://dx.doi.org/10.1073/pnas.1005556107
  14. Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA. Crystal structure of a self-splicing group I intron with both exons. Nature. 2004 Jul 1;430(6995):45-50. Epub 2004 Jun 2. PMID:15175762 doi:10.1038/nature02642
  15. Stahley MR, Strobel SA. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science. 2005 Sep 2;309(5740):1587-90. PMID:16141079 doi:309/5740/1587
  16. Lipchock SV, Strobel SA. A relaxed active site after exon ligation by the group I intron. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5699-704. Epub 2008 Apr 11. PMID:18408159
  17. Antonioli AH, Cochrane JC, Lipchock SV, Strobel SA. Plasticity of the RNA kink turn structural motif. RNA. 2010 Apr;16(4):762-8. Epub 2010 Feb 9. PMID:20145044 doi:10.1261/rna.1883810
  18. Chao JA, Williamson JR. Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Structure. 2004 Jul;12(7):1165-76. PMID:15242593 doi:10.1016/j.str.2004.04.023
  19. Montange RK, Batey RT. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature. 2006 Jun 29;441(7097):1172-5. PMID:16810258 doi:10.1038/nature04819
  20. Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001 Nov 30;107(5):679-88. PMID:11733066
  21. Chen YW, Bycroft M, Wong KB. Crystal structure of ribosomal protein L30e from the extreme thermophile Thermococcus celer: thermal stability and RNA binding. Biochemistry. 2003 Mar 18;42(10):2857-65. PMID:12627951 doi:10.1021/bi027131s
  22. Wong KB, Lee CF, Chan SH, Leung TY, Chen YW, Bycroft M. Solution structure and thermal stability of ribosomal protein L30e from hyperthermophilic archaeon Thermococcus celer. Protein Sci. 2003 Jul;12(7):1483-95. PMID:12824494 doi:10.1110/ps.0302303
  23. Gagnon MG, Steinberg SV. The adenosine wedge: a new structural motif in ribosomal RNA. RNA. 2010 Feb;16(2):375-81. Epub 2009 Dec 28. PMID:20038632 doi:10.1261/rna.1550310
  24. Steinberg SV, Boutorine YI. G-ribo: a new structural motif in ribosomal RNA. RNA. 2007 Apr;13(4):549-54. Epub 2007 Feb 5. PMID:17283211 doi:10.1261/rna.387107
  25. Lee JC, Cannone JJ, Gutell RR. The lonepair triloop: a new motif in RNA structure. J Mol Biol. 2003 Jan 3;325(1):65-83. PMID:12473452
  26. Tamura M, Holbrook SR. Sequence and structural conservation in RNA ribose zippers. J Mol Biol. 2002 Jul 12;320(3):455-74. PMID:12096903

Additional Literature and External Resources

  • Schroeder KT, McPhee SA, Ouellet J, Lilley DM. A structural database for k-turn motifs in RNA. RNA. 2010 Aug;16(8):1463-8. Epub 2010 Jun 18. PMID:20562215 doi:10.1261/rna.2207910
  • Tiedge H. K-turn motifs in spatial RNA coding. RNA Biol. 2006 Oct;3(4):133-9. Epub 2006 Oct 31. PMID:17172877

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