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User:Wayne Decatur/kink-turn motif

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==Structures Containing the Motif==
==Structures Containing the Motif==
<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' />
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* [[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>. 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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* [[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>.
* [[1e7k]] – the spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to a U4 snRNA fragment<ref>PMID: 11163207</ref>
* [[1e7k]] – the spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to a U4 snRNA fragment<ref>PMID: 11163207</ref>
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* [[1nkw]] – The Large Ribosomal Subunit From ''Deinococcus radiodurans''
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* Small Ribosomal Subunit
==See Also==
==See Also==
* [http://www.dundee.ac.uk/biocentre/nasg/kturn/index.php Kink-turns in RNA] - a structural database for k-turn motifs in RNA by the Lilley group<ref name="lilleydatabase" />
* [http://www.dundee.ac.uk/biocentre/nasg/kturn/index.php Kink-turns in RNA] - a structural database for k-turn motifs in RNA by the Lilley group<ref name="lilleydatabase" />
* [[Ribosome]]
* [[Ribosome]]
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* [[Large Ribosomal Subunit of Haloarcula]]
 
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* Small Ribosomal Subunit
 
* [[1cn7]], [[1go1]], [[1go0]], [[1w3e]] and [[1h7m]] – the yeast ribosomal protein L30<ref>PMID: 10581556</ref><ref>PMID: 12627951</ref><ref>PMID: 12824494</ref> binds a kink-turn motif
* [[1cn7]], [[1go1]], [[1go0]], [[1w3e]] and [[1h7m]] – the yeast ribosomal protein L30<ref>PMID: 10581556</ref><ref>PMID: 12627951</ref><ref>PMID: 12824494</ref> binds a kink-turn motif
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* [[1nkw]] – The Large Ribosomal Subunit From ''Deinococcus radiodurans''
 
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* [[3cc2]]
 
* A-minor motif
* A-minor motif
* The adenosine wedge motif<ref>PMID: 20038632</ref>
* The adenosine wedge motif<ref>PMID: 20038632</ref>

Revision as of 05:01, 1 August 2010

WHEN MADE INTO AN OFFICIAL PAGE:

  • 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].
  • 1e7k – the spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to a U4 snRNA fragment[4]
  • 1nkw – The Large Ribosomal Subunit From Deinococcus radiodurans
  • 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. ↑ Mao H, White SA, Williamson JR. A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nat Struct Biol. 1999 Dec;6(12):1139-47. PMID:10581556 doi:10.1038/70081
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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

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

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Jaime Prilusky, Joel L. Sussman

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