This entry represents the RNA recognition motif (RRM) of budding yeast Nrd1 and fission yeast Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein. It is part of the Nrd1-Nab3-Sen1 (NNS) complex that is involved in the termination and processing of short RNA polymerase II transcripts [].Nrd1 contains an RNA recognition motif (RRM), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable [].Seb1 is an RNA-binding protein essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 does not function in NNS-like termination. Instead, Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection []. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain) [].
This entry represents the RNA recognition motif 1 (RRM1) in Mrn1. Proteins containing this motif also include S. pombe Nrd1 (also known as Msa2), which inhibits sexual differentiation []. Mrn1 is an RNA binding protein that localizes both to the nucleus and cytoplasm. It may be involved in the mRNA processing pathway []. Mrn1 contains four copies of a conserved RNA recognition motif (RRM).
This entry includes fungal Sen1. The yeast helicase Sen1 is a subunit of the Nrd1 complex (Nrd1-Nab3-Sen1), which interacts with the exosome to mediate 3' end formation of some mRNAs, snRNAs and snoRNAs []. In Schizosaccharomyces pombe, Sen1 functions as an ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs [, ]. It may also play a role in transcription-coupled nucleotide excision repair [].
This entry represents the RNA recognition motif 4 of ROD1 (also known as polypyrimidine tract-binding protein 3, PTBP3), which is an RNA-binding protein highly expressed in hematopoietic cells []. It is a functional homologue of fission yeast Nrd1 and may be involved in differentiation control []. It also plays a role in nonsense-mediated mRNA decay (NMD) []. Several ROD1 isoforms can be generated by alternative splicing and translation initiation []. Rod1 contains four repeats of RNA recognition motifs (RRM).
This entry represents the RNA recognition motif 1 of ROD1 (also known as polypyrimidine tract-binding protein 3, PTBP3), which is an RNA-binding protein highly expressed in hematopoietic cells []. It is a functional homologue of fission yeast Nrd1 and may be involved in differentiation control []. It also plays a role in nonsense-mediated mRNA decay (NMD) []. Several ROD1 isoforms can be generated by alternative splicing and translation initiation []. Rod1 contains four repeats of RNA recognition motifs (RRM).
This entry represents the RNA recognition motif (RRM) of Nab3p (also known as Hmd1p), an acidic nuclear polyadenylated RNA-binding protein that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in budding yeast []. It plays an important role in the maintenance of CLN3 mRNA levels []. It is part of the Nrd1 complex (Nrd1p-Nab3p-Sen1p) that directs the termination and processing of short RNA polymerase II transcripts and regulates cellular response to nutrient availability []. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), and a C-terminal region rich in glutamine and proline residues [].
The C-terminal domain (CTD) of the large subunit of RNA polymerase II is aplatform for mRNA processing factors and links gene transcription to mRNAcapping, splicing and polyadenylation. CTD recognition is dependent on thephosphorylation state of the CTD itself, which varies during the course oftranscription but has also been linked to the isomerization state of the CTD'sproline residues. Several RNA-processing factors recognise the CTD by means ofa conserved CTD-interacting domain (CID). Factors with CID domains include theserine/arginine-rich-like factors SCAF4 and SCAF8, Nrd1 (which is implicatedin polyadenylation-independent RNA 3'-end formation) and Pcf11. Pcf11 is aconserved and essential subunit of the yeast cleavage factor 1A, which isrequired for 3'-RNA processing and transcription termination [, ].The CID domain is a right-handed superhelix of eight α-helices forming acompact domain. The CID fold closely resembles that of VHSdomains and is related to armadillo-repeat proteins , except for the two amino-terminal helices. Amino acid residuesin the hydrophobic core of the domain are highly conserved across CID domains[, ].
