User:Wayne Decatur/kink-turn motif

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The kink-turn motif
A common RNA structural motif that consists of helix–internal loop–helix motif .

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

• 1e7k – the spliceosomal and snoRNP 15.5kD protein bound to a U4 snRNA fragment^[3]

See Also

• Ribosome
• Large Ribosomal Subunit of Haloarcula
• Small Ribosomal Subunit
• 1cn7, 1go1, 1go0, 1w3e and 1h7m – the yeast ribosomal protein L30^[4][5][6] binds a kink-turn motif
• 1nkw – The Large Ribosomal Subunit From Deinococcus radiodurans

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. ↑ 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
4. ↑ 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
5. ↑ 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
6. ↑ 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

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

• RCSB Protein Data Bank coverage of the 2009 Nobel Prizes in Chemistry
• 70S Ribosome: January 2010 Molecule of the Month as part of the series of tutorials that are at the RCSB Protein Data Bank and written by David Goodsell
• Ribosome: October 2000 Molecule of the Month as part of the series of tutorials that are at the RCSB Protein Data Bank and written by David Goodsell
• The structure of the large ribosomal subunit revealed many motifs now known to be common in other rRNAs. The kink-turn, or k-turn, is one such example^[23]. Those in the Haloarcula large ribosomal subunit are shown clearly in Jmol by following the appropriate links on this page at a structural database for k-turn motifs in RNA by the Lilley group, although where they are in the context of the entire subunit is not presented.