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NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding

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journal contribution
posted on 25.03.2008, 00:00 by Jampani Nageswara Rao, Kristian Schweimer, Sabine Wenzel, Birgitta M. Wöhrl, Paul Rösch
The E subunit of the human heterotetrameric negative transcription elongation factor (NELF-E) contains a canonical βαββαβ RNA recognition motif (RRM) that binds to a wide variety of RNA sequences. These induce very similar conformational changes in the RRM as determined by nuclear magnetic resonance spectroscopy. Although the RNA binding interface of a canonical RRM is mainly located at its β-sheet surface, for NELF-E RRM large chemical shift perturbations are observed for residues in the flexible C-terminal region and the loop between β3 and α2, and both regions are distant from the interface. We determined the solution structure of single-stranded transactivator responsive element (TAR) RNA-bound NELF-E RRM. This structure clearly shows that RNA binding to NELF-E RRM induces formation of a helix in the C-terminus. The RNA-bound form of NELF-E RRM is very similar to the RNA-bound form of U1A RRM, although the C-terminus of the NELF-E RRM is unstructured in the free protein, whereas it is helical in the U1A protein. Thus, RNA binding to NELF-E RRM induces a conformational change toward the U1A structure, resulting in highly similar RNA binding conformations for both proteins.

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