2 edition of RNA recognition by SAM domains found in the catalog.
RNA recognition by SAM domains
Written in English
Anteroposterior patterning in Drosophila melanogaster is dependent upon the sequence-specific RNA binding protein Smaug, which binds to and regulates the translation of nanos mRNA. In this thesis, I demonstrate that the s&barbelow;terile-a&barbelow;lpha m&barbelow;otif (SAM) domain of Smaug functions as an RNA recognition domain. This represents a new function for the SAM domain family, which is well characterized for mediating protein-protein interactions. Using homology modeling and site-directed mutagenesis, I have localized the RNA binding surface of the Smaug SAM domain. The conservation of these surface residues in a group of SAM domain containing proteins present from yeast to human suggested that these proteins share a common RNA binding function. I proved this point by demonstrating that the SAM domain of the Smaug homolog in Saccharomyces cerevisiae (Vts1) binds RNA hairpins with essentially the same affinity and sequence specificity as Smaug. In addition, I solved the crystal structures of the Vts1 SAM domain in its unliganded state and in complex with an RNA hairpin. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Specificity of hairpin binding arises from the association of a guanosine base of the hairpin loop with a shallow pocket on the SAM domain and from multiple contacts made to the unique backbone structure of the hairpin. Using a reporter gene, I demonstrated that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. Subsequentially, I validated NNF1 as an endogenous target of Vts1 among 79 transcripts that co-purify with epitope tagged Vts1. Together my work uncovers the molecular details of sequence-specific RNA recognition by a conserved subfamily of SAM domains and define a class of post-transcriptional regulators that act in part through a common RNA binding mechanism.
|Statement||by Tzvi Aviv.|
|The Physical Object|
|Pagination||xi, 142 leaves.|
|Number of Pages||142|
Molecular Cell Resource Comprehensive Identiﬁcation of RNA-Binding Domains in Human Cells Alfredo Castello,1,2,5 Bernd Fischer,1,3,5 Christian K. Frese,1 Rastislav Horos,1 Anne-Marie Alleaume,1 Sophia Foehr,1 Tomaz Curk, 1,4 Jeroen Krijgsveld, 3 and Matthias W. Hentze1,* 1European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res. ; ; Display abstract; We present a systematic analysis of sequence motifs found in metazoan protein factors involved in constitutive pre-mRNA splicing and in alternative splicing regulation.
5.^ A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein. Query CC, Bentley RC, Keene JD. C , (). Rfam (April , families) The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus .
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool. Spahr et al. () reported that NSUN4 contains a typical 5-methylcytosine RNA methyltransferase core domain with active-site residues necessary for recognition of the S-adenosyl-L-methionine (SAM) cosubstrate and for methyltransferase activity. However, NSUN4 lacks variable N- or C-terminal extensions required for RNA recognition in related.
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RNA recognition via the SAM domain of Smaug. The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug.
We report here the crystal structure of the Smaug RNA binding domain, which shows no sequence homology to any previously characterized RNA binding motif.
The putative yeast post-transcriptional regulator Vts1p and its related protein Smaug, from Drosophila melanogaster, each use a sterile alpha motif (SAM) domain to bind an RNA recognition by SAM domains book hairpin termed the Smaug recognition element (SRE).
Here, we present the NMR structures of the Vts1p-SRE complex and the fre RNA recognition by the Vts1p SAM domainCited by: Finally, we show that an isolated SAM domain of Smg is capable of recognizing the TCE hairpin specifically, and that this RNA binding function is preserved in homologous SAM domains from mouse and frog.
Taken together, this structural, genetic, and evolutionary evidence identifies a subfamily of SAM domains with an RNA binding by: RNA recognition by the Vts1p SAM domain | Nature Structural & Molecular Biology The putative yeast post-transcriptional regulator Vts1p and its related protein Smaug, from Drosophila melanogaster, Cited by: Unexpectedly, we find through a combination of structural and genetic analysis that it is primarily the SAM domain that interacts specifically with the appropriate nanos mRNA regulatory sequence.
Therefore, in addition to their previously characterized roles in protein-protein interactions, some SAM domains play crucial roles in RNA by: Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.
RNA Recognition via the SAM Domain of Smaug Previous Article TbMP57 Is a 3′ Terminal Uridylyl Transferase (TUTase) of the Trypanosoma brucei Editosome Next Article Structure of an mRNA Capping Enzyme Bound to the Phosphorylated Carboxy-Terminal Domain of RNA Polymerase II.
Single-Stranded RNA Recognition Domains. Cite this entry as: () RNA Recognition Domains. In: Roberts G.C.K. (eds) Encyclopedia of Biophysics.
Indeed, protein domains such as zinc fingers [12–14], SAM domains [15,16], Z-DNA/Z-RNA binding domains [17–19], or even RRM domains [20–23], are also known to recognize RNA modules containing dsRNA fragments, such as regular dsRNA fragments, left-handed Z-RNA helices or short RNA hairpins.
This review concentrates on dsRBDs and readers. RNA recognition by ssRNA binding proteins is a core event in mRNA metabolism that confers specificity to regulatory mechanisms and allows the coordination of the different steps of mRNA synthesis, processing, export, localization, translation, and degradation.
Most ssRNA binding domains are relatively small (40– amino acids). To further understand the function of SAM-RNA recognition, we determined the solution structures of the SAM domain of the Saccharomyces cerevisiae Vts1p (Vts1p-SAM) and the Smaug response element.
RNA Recognition via the SAM Domain of Smaug. By Brain Tumor (brat, Cary D. Gardner, Robin P. Wharton, Aneel K. Aggarwal, Dominal Segmentation (chagnovich and. rna recognition sam domain sequence homology rna binding domain amino acid crystal structure proper abdominal segmentation large protein wild-type tce domain consisting subsequent study north carolina smaug rna loop sequence cuggc normal smg function tce hairpin duke university medical center pin no mrna head development sufficient tovia.
Structure of the RNA_GG_bind domain from C. parvum. We solved the crystal structure of the CpGGBD using selenomethionyl substituted protein by the MAD method at Å in one P2 1 crystal form. The native structure was refined at Å in a second P2 1 crystal form to an R-factor (R-free) of () (Tables 1,2).
2).Both crystal forms contain four molecules in the asymmetric unit. The recognition of the RNA substrate, primarily through its triphosphate moiety, could explain the activity of the TTM RTPase against NTP substrates. Interestingly, this NTP hydrolysis is not supported by Mg 2+, but is rather dependent on Mn 2+ or Co 2+.
The coordinated metal ion, in conjunction with basic lysine and arginine, activates the γ. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards.
The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
the only protein domain known to bind to dsRNA modules. Indeed, protein domains such as zinc fingers , SAM domains [15,16], Z-DNA/Z-RNA binding domains , or even RRM domains , are also known to recognize RNA modules containing dsRNA fragments, such as regular dsRNA fragments, left-handed Z-RNA helices or short RNA hairpins.
The NMR and X-ray Structures of the Saccharomyces cerevisiae Vts1 SAM Domain Define a Surface for the Recognition of RNA Hairpins. Journal of Molecular Biology(2), DOI: / The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by report here the crystal structure of the Smaug RNA binding domain, which shows no sequence homology to any previously characterized RNA binding motif.
The structure reveals an unusual makeup in which a SAM domain, a common protein. RNA recognition via the SAM domain of Smaug. Mol Cell. ; ; Display abstract; The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug.
We report here the crystal structure of the Smaug RNA binding domain, which shows no sequence. Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains.RNA recognition motif, RNP-1 is a putative RNA-binding domain of about 90 amino acids that are known to bind single-stranded RNAs.
It was found in many eukaryotic proteins.   .COMMUNICATION The NMR and X-ray Structures of the Saccharomyces cerevisiae Vts1 SAM Domain Deﬁne a Surface for the Recognition of RNA Hairpins Tzvi Aviv1,2, Andrew N. Amborski 3, X. Sharon Zhao, Jamie J. Kwan4 Philip E. Johnson3, Frank Sicheri1,2* and Logan W.
Donaldson4* 1Program in Molecular Biology and Cancer, Samuel Lunenfeld.