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User:Wayne Decatur/kink-turn motif

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<applet load='Image:Kt7.pdb.gz' size='400' frame='true' align='right' scene='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/2' />
<applet load='Image:Kt7.pdb.gz' size='400' frame='true' align='right' scene='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/2' />
* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] contains 8 identified kink-turns: <scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/2'>Kt-7</scene>,Kt-58 of [[3cc2]]. MAKE '''The location of all of them in the subunit.''' To see them 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">PMID: 20562215</ref>.
* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] contains 8 identified kink-turns: <scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/2'>Kt-7</scene>,Kt-58 of [[3cc2]]. MAKE '''The location of all of them in the subunit.''' To see them 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">PMID: 20562215</ref>.
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* [[1e7k]] – the human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to a U4 spliceosomal RNA fragment<ref>PMID: 11163207</ref>
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* The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to a U4 spliceosomal RNA fragment ([[1e7k]])<ref>PMID: 11163207</ref>
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* [[1rlg]] - ''A. fulgidus'' small ribonucleoprotein particle box C/D RNA complexed with L7Ae<ref>PMID: 15130473</ref>
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* ''A. fulgidus'' small ribonucleoprotein particle box C/D RNA complexed with L7Ae ([[1rlg]])<ref>PMID: 15130473</ref>
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* [[2hvy]] - ''Pyrococcus furiosus'' small ribonucleoprotein particle H/ACA box RNA from <ref>PMID: 16943774</ref>
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* ''Pyrococcus furiosus'' small ribonucleoprotein particle H/ACA box RNA [[2hvy]])<ref>PMID: 16943774</ref>
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* [[1u6b]], [[1zzn]], [[3bo2]], [[3bo3]], [[3bo4]], and [[3iin]] - ''Azoarcus'' group I intron has a 'reverse' kink-turn'''PUT A SCENE HERE OF ALIGNMENT OF THIS WITH KT-T COLORED SO CLEAR WHAT IS WHAT BETTER THAN SEEN AT KINK-TURN DATABASE<ref>PMID: 15175762</ref><ref>PMID: 16141079</ref><ref> PMID:18408159</ref><ref>PMID:20145044</ref>
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* ''Azoarcus'' group I intron has a 'reverse' kink-turn'''PUT A SCENE HERE OF ALIGNMENT OF THIS WITH KT-7 with each Kt colored differently [[1u6b]], [[1zzn]], [[3bo2]], [[3bo3]], [[3bo4]], and [[3iin]]<ref>PMID: 15175762</ref><ref>PMID: 16141079</ref><ref> PMID:18408159</ref><ref>PMID:20145044</ref>
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* [[1t0k]] - ''S. cervisiae'' L30e bound to its pre-mRNA<ref>PMID: 15242593</ref>
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* ''S. cervisiae'' L30e bound to its pre-mRNA [[1t0k]]<ref>PMID: 15242593</ref>
* [[1nkw]] – The Large Ribosomal Subunit From ''Deinococcus radiodurans''<ref> PMID:11733066</ref>
* [[1nkw]] – The Large Ribosomal Subunit From ''Deinococcus radiodurans''<ref> PMID:11733066</ref>
* Small Ribosomal Subunit
* Small Ribosomal Subunit

Revision as of 01:38, 2 August 2010

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 .


Contents

Introduction

Originally identified in the course of analyzing the large ribosomal subunit[1], the motif was identified in other RNAs. Particular instances are referred to as the the GA motif [2] A motif that includes the A-minor motif. Many K-turns bind proteins; however, they also mediate RNA tertiary structure interactions.

Structures Containing the Motif

Drag the structure with the mouse to rotate
  • The Large Ribosomal Subunit contains 8 identified kink-turns: ,Kt-58 of 3cc2. MAKE The location of all of them in the subunit. To see them 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 a U4 spliceosomal RNA fragment (1e7k)[4]
  • A. fulgidus small ribonucleoprotein particle box C/D RNA complexed with L7Ae (1rlg)[5]
  • Pyrococcus furiosus small ribonucleoprotein particle H/ACA box RNA 2hvy)[6]
  • Azoarcus group I intron has a 'reverse' kink-turnPUT A SCENE HERE OF ALIGNMENT OF THIS WITH KT-7 with each Kt colored differently 1u6b, 1zzn, 3bo2, 3bo3, 3bo4, and 3iin[7][8][9][10]
  • S. cervisiae L30e bound to its pre-mRNA 1t0k[11]
  • 1nkw – The Large Ribosomal Subunit From Deinococcus radiodurans[12]
  • Small Ribosomal Subunit

See Also

References

  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 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. ↑ 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. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
  13. ↑ 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
  14. ↑ 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
  15. ↑ 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
  16. ↑ 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
  17. ↑ 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
  18. ↑ 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 Resources

  • Moore PB. The ribosome returned. J Biol. 2009;8(1):8. Epub 2009 Jan 26. PMID:19222865 doi:10.1186/jbiol103
  • Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008 Mar;9(3):242-53. PMID:18292779 doi:10.1038/nrm2352
  • Rodnina MV, Wintermeyer W. The ribosome goes Nobel. Trends Biochem Sci. 2010 Jan;35(1):1-5. Epub 2009 Dec 2. PMID:19962317 doi:10.1016/j.tibs.2009.11.003
  • Schmeing TM, Ramakrishnan V. What recent ribosome structures have revealed about the mechanism of translation. Nature. 2009 Oct 29;461(7268):1234-42. Epub 2009 Oct 18. PMID:19838167 doi:10.1038/nature08403
  • Ramakrishnan V, Moore PB. Atomic structures at last: the ribosome in 2000. Curr Opin Struct Biol. 2001 Apr;11(2):144-54. PMID:11297922
  • 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

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Wayne Decatur, Joel L. Sussman

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