2M88
NMR structure of a two-domain RNA-binding fragment of Nrd1
Summary for 2M88
| Entry DOI | 10.2210/pdb2m88/pdb |
| NMR Information | BMRB: 19232 |
| Descriptor | Protein NRD1 (1 entity in total) |
| Functional Keywords | nrd1 complex, rna processing and degradation, rrm structure, rna binding protein |
| Biological source | Saccharomyces cerevisiae (Baker's yeast) |
| Cellular location | Nucleus (Potential): P53617 |
| Total number of polymer chains | 1 |
| Total formula weight | 21799.60 |
| Authors | Bacikova, V.,Pasulka, J.,Kubicek, K.,Stefl, R. (deposition date: 2013-05-08, release date: 2014-05-14, Last modification date: 2024-05-15) |
| Primary citation | Bacikova, V.,Pasulka, J.,Kubicek, K.,Stefl, R. Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Res., 42:8024-8038, 2014 Cited by 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: 24860164DOI: 10.1093/nar/gku446 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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