User:Wayne Decatur/kink-turn motif

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Originally identified in the course of analyzing the [[Large Ribosomal Subunit of Haloarcula|large ribosomal subunit]]<ref name="kleinref">PMID: 11483524</ref>, this RNA structural motif was also identified in other RNAs. Particular instances have been called the GA motif <ref>PMID: 11497434</ref>
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[[kink-turn motif|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. Originally identified in the course of analyzing the [[Large Ribosomal Subunit of Haloarcula|large ribosomal subunit]]<ref name="kleinref">PMID: 11483524</ref>, this RNA structural motif was also identified in other RNAs. Particular instances have been called the GA motif <ref>PMID: 11497434</ref>.
The kink-turn motif includes the [[A-minor motif]].
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.
Many kink-turns bind proteins; however, that trait is not universal. They can mediate RNA tertiary structure interactions as well.

Revision as of 22:07, 15 May 2011

  UNDER DEVELOPMENT: This article is a work in progress, and is incomplete.  
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WHEN MADE INTO AN OFFICIAL PAGE:

  • LINK FROM RNA motifs PAGE!!!!
  • Fix links from and to large ribosomal subunit (AND RIBOSOME?) page
  • Fix link from topic pages and from table of contents
  • add Redirect from K-turn motif
  • add redirect from GA motif
  • add redirect from kink-turn
  • add redirect from k-turn


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

 
Drag the structure with the mouse to rotate

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. 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].

Structures Containing the Motif

 

Drag the structure with the mouse to rotate

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)[4]. 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[5][4] 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)[6]. .
  • A. fulgidus small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae (1rlg)[7] has a kink turn.
  • Pyrococcus furiosus small ribonucleoprotein particle box H/ACA RNA (2hvy[8],3hax,3hay[9]) has a kink turn that is bound directly by L7ae in a complex of several proteins.
  • Azoarcus group I intron (1u6b, 1zzn, 3bo2, 3bo3, 3bo4, and 3iin)[10][11][12][13] 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
  • S. cervisiae L30e bound to its pre-mRNA (1t0k)[14] has a kink-turn with a protein bound.
  • S-adenosylmethionine riboswitch regulatory mRNA element from Thermoanaerobacter tengcongensis (2gis)[15] 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[16]
  • 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. ↑ 4.0 4.1 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
  13. ↑ 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
  14. ↑ 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
  15. ↑ 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
  16. ↑ 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
  17. ↑ 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
  18. ↑ 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
  19. ↑ 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
  20. ↑ 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
  21. ↑ 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
  22. ↑ 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

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Jaime Prilusky, Joel L. Sussman

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