Chapter 11

RNA Tertiary Structure and Protein Recognition in an L11-RNA Complex

David E. Draper

David E. Draper

Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218

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Graeme L. Conn

Graeme L. Conn

Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218

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Apostolos G. Gittis

Apostolos G. Gittis

Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218

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Debraj Guhathakurta

Debraj Guhathakurta

Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218

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Eaton E. Lattman

Eaton E. Lattman

Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218

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Luis Reynaldo

Luis Reynaldo

Third Wave Technologies, Inc., 502 South Rosa Rd., Madison, WI, 53719

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First published: 27 March 2000

Summary

This chapter relates the intricate architecture of the L11-RNA complex to previous studies that delineated crucial features of the RNA tertiary structure and protein-RNA interface. In describing the structure, it is interesting to note how conservation and variation of different nucleotides and amino acids serve as a guide to critical features of the complex, and the authors use the extreme conservation of some bases to speculate about functional surfaces of the rRNA domain. Lastly, the chapter discusses the possibility that the functional role of L11-C76 is to promote a correct RNA tertiary fold. Relatively few RNA structures that have noncanonical interactions have been determined at atomic resolution, and of these only tRNA and the P4-P6 domain of group I intron have extensive tertiary structure. From nuclear magnetic resonance (NMR) studies of the free L11 RNA binding domain (L11-C76), it was known that the protein folds into three α-helices that are superimposable on the α-helices of the homeodomain class of DNA binding proteins. Covariation analysis has been an extremely powerful method for predicting rRNA secondary structure and providing clues to tertiary interactions. In melting studies of the 58-nt RNA, it was proposed that the lowest-temperature melting transition is due to unfolding of a set of tertiary interactions that link the three helical elements. In the last decade rRNA has taken center stage as the functional component of ribosomes, and it has been suggested that the primary role of ribosomal proteins is to promote RNA folding.

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