View source for 2m88


==NMR structure of a two-domain RNA-binding fragment of Nrd1==
<StructureSection load='2m88' size='340' side='right'caption='[[2m88]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2m88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M88 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2m88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m88 OCA], [https://pdbe.org/2m88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m88 RCSB], [https://www.ebi.ac.uk/pdbsum/2m88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m88 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.

Structure and semi-sequence-specific RNA binding of Nrd1.,Bacikova V, Pasulka J, Kubicek K, Stefl R Nucleic Acids Res. 2014 Aug 1;42(12):8024-38. doi: 10.1093/nar/gku446. Epub 2014 , May 23. PMID:24860164<ref>PMID:24860164</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2m88" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Bacikova V]]
[[Category: Kubicek K]]
[[Category: Pasulka J]]
[[Category: Stefl R]]