User:Wayne Decatur/kink-turn motif: Difference between revisions

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:* See all of the 23S rRNA kink-turns and others on this page in greater detail following the appropriate links on [http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_known.php this page at a structural database for k-turn motifs in RNA by the Lilley group]<ref name="lilleydatabase" />.
:* See all of the 23S rRNA kink-turns and others on this page in greater detail following the appropriate links on [http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_known.php this page at a structural database for k-turn motifs in RNA by the Lilley group]<ref name="lilleydatabase" />.
*  The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to the kink-turn of a U4 spliceosomal RNA fragment ([[1e7k]])<ref name="u4xstal">PMID: 11163207</ref>. 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<ref>PMID: 11081632</ref><ref name="u4xstal" /> even before the kink-turn was shown to be a widespread motif.
*  The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to the kink-turn of a U4 spliceosomal RNA fragment ([[1e7k]])<ref name="u4xstal">PMID: 11163207</ref>. 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<ref>PMID: 11081632</ref><ref name="u4xstal" /> even before the kink-turn was shown to be a widespread motif.
* The <scene name='Sandbox3pla/Proteincolored/4'>box C/D RNP</scene> from ''Sulfolobus solfataricus'' has two kink-turns that bound by L7Ae ([[3pla]])<ref>PMID: 21270896</ref>.
* The <scene name='User:Wayne_Decatur/kink-turn_motif/Proteincolored/1'>box C/D RNP</scene> from ''Sulfolobus solfataricus'' has two kink-turns that bound by L7Ae ([[3pla]])<ref>PMID: 21270896</ref>. {{Link Toggle FancyCartoonHighQualityView}}.
* ''A. fulgidus'' small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae ([[1rlg]])<ref>PMID: 15130473</ref> has a kink turn.   
* ''A. fulgidus'' small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae ([[1rlg]])<ref>PMID: 15130473</ref> has a kink turn.   
* ''Pyrococcus furiosus'' small ribonucleoprotein particle box H/ACA RNA ([[2hvy]]<ref>PMID: 16943774</ref>,[[3hax]],[[3hay]]<ref>PMID: 19481523</ref>) has a kink turn that is bound directly by L7ae in a complex of several proteins.
* ''Pyrococcus furiosus'' small ribonucleoprotein particle box H/ACA RNA ([[2hvy]]<ref>PMID: 16943774</ref>,[[3hax]],[[3hay]]<ref>PMID: 19481523</ref>) has a kink turn that is bound directly by L7ae in a complex of several proteins.

Revision as of 01:26, 9 February 2011

WHEN MADE INTO AN OFFICIAL PAGE:

  • LINK FROM RNA motifs 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.


Introduction

 
Drag the structure with the mouse to rotate

A C G U

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 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 motif.
  • The box C/D RNP from Sulfolobus solfataricus has two kink-turns that 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:https://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:https://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:https://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

  1. 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
  1. Tiedge H. K-turn motifs in spatial RNA coding. RNA Biol. 2006 Oct;3(4):133-9. Epub 2006 Oct 31. PMID:17172877
  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named lilleydatabase

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Wayne Decatur, Joel L. Sussman, Jaime Prilusky

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