Nucleic Acids Research Advance Access originally published online on December 14, 2006
Nucleic Acids Research 2007 35(2):441-454; doi:10.1093/nar/gkl1066
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Nucleic Acids Research, 2007, Vol. 35, No. 2 441-454
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy
1 Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany 2 University of Texas Health Science Center SA, Department of Biochemistry 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
*To whom correspondence should be addressed. Tel: +69 7982 9737; Fax: +69 7982 9515; Email: schwalbe{at}nmr.uni-frankfurt.de
Received October 11, 2006. Revised November 20, 2006. Accepted November 20, 2006.
Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11ctd). In addition, the N-terminal domain of L11 (L11ntd) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11ntd, placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11–RNA–thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11ntd in elongation factor binding.
*Correspondence may also be addressed to Jens Wöhnert. Tel: +1 210 567 3743; Fax: +1 210 567 6595; Email: jewoe{at}biochem.uthscsa.edu
Present address: Serge Ilin, Sloan-Kettering Institute, Structural Biology Program, 1275 York Avenue, New York, NY 10021, USA
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