2M88

NMR structure of a two-domain RNA-binding fragment of Nrd1

2M88 の概要

• エントリーDOI: 10.2210/pdb2m88/pdb
• NMR情報: BMRB: 19232
• 分子名称: Protein NRD1 (1 entity in total)
• 機能のキーワード: nrd1 complex, rna processing and degradation, rrm structure, rna binding protein
• 由来する生物種: Saccharomyces cerevisiae (Baker's yeast)
• 細胞内の位置: Nucleus (Potential): P53617
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 21799.60

構造登録者

Bacikova, V.,Pasulka, J.,Kubicek, K.,Stefl, R. (登録日: 2013-05-08, 公開日: 2014-05-14, 最終更新日: 2024-05-15)

主引用文献

Bacikova, V.,Pasulka, J.,Kubicek, K.,Stefl, R.
Structure and semi-sequence-specific RNA binding of Nrd1.
Nucleic Acids Res., 42:8024-8038, 2014

PubMed Abstract: In Saccharomyces cerevisiae, the Nrd1-dependent termination and processing pathways play an important role in surveillance and processing of non-coding ribonucleic acids (RNAs). The termination and subsequent processing is dependent on the Nrd1 complex consisting of two RNA-binding proteins Nrd1 and Nab3 and Sen1 helicase. It is established that Nrd1 and Nab3 cooperatively recognize specific termination elements within nascent RNA, GUA[A/G] and UCUU[G], respectively. Interestingly, some transcripts do not require GUA[A/G] motif for transcription termination in vivo and binding in vitro, suggesting the existence of alternative Nrd1-binding motifs. Here we studied the structure and RNA-binding properties of Nrd1 using nuclear magnetic resonance (NMR), fluorescence anisotropy and phenotypic analyses in vivo. We determined the solution structure of a two-domain RNA-binding fragment of Nrd1, formed by an RNA-recognition motif and helix-loop bundle. NMR and fluorescence data show that not only GUA[A/G] but also several other G-rich and AU-rich motifs are able to bind Nrd1 with affinity in a low micromolar range. The broad substrate specificity is achieved by adaptable interaction surfaces of the RNA-recognition motif and helix-loop bundle domains that sandwich the RNA substrates. Our findings have implication for the role of Nrd1 in termination and processing of many non-coding RNAs arising from bidirectional pervasive transcription.

PubMed: 24860164
DOI: 10.1093/nar/gku446

実験手法

SOLUTION NMR