NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding.
The E subunit of the human heterotetrameric negative transcription elongation factor (NELF-E) contains a canonical betaalphabetabetaalphabeta 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 beta-sheet surface, for NELF-E RRM large chemical shift perturbations are observed for residues in the flexible C-terminal region and the loop between beta 3 and alpha 2, 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.
Rao
Jampani Nageswara
JN
Lehrstuhl Biopolymere and Research Center for Bio-Macromolecules, Universität Bayreuth, 95440 Bayreuth, Germany.
Schweimer
Kristian
K
Wenzel
Sabine
S
Wöhrl
Birgitta M
BM
Rösch
Paul
P
D020816:Amino Acid Motifs; D001483:Base Sequence; D006801:Humans; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D016601:RNA-Binding Proteins / Q000737:chemistry*; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000737:chemistry; D014157:Transcription Factors; D035602:Transcriptional Elongation Factors / Q000737:chemistry*; D000099253:Trans-Activation Responsive RNA-Binding Protein
D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; D017412:Ribonucleoprotein, U1 Small Nuclear; D014157:Transcription Factors; D035602:Transcriptional Elongation Factors; C071598:TARBP1 protein, human; D000099253:Trans-Activation Responsive RNA-Binding Protein; C075339:U1A protein; C118437:negative elongation factor