3QGB

Crystal structure of FBF-2 R288Y mutant in complex with gld-1 FBEa

Summary for 3QGB

• Entry DOI: 10.2210/pdb3qgb/pdb
• Related: 3K5Y 3QG9 3QGC
• Descriptor: Fem-3 mRNA-binding factor 2, 5'-R(*UP*GP*UP*GP*CP*CP*AP*UP*A)-3' (3 entities in total)
• Functional Keywords: fbf, fem-3 binding factor, puf, rna-binding specificity, base stacking, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Caenorhabditis elegans (nematode); More
• Cellular location: Cytoplasm (By similarity): Q09312
• Total number of polymer chains: 2
• Total formula weight: 49857.76

Authors

Wang, Y.,Qiu, C.,Koh, Y.Y.,Opperman, L.,Gross, L.,Hall, T.M.T.,Wickens, M. (deposition date: 2011-01-24, release date: 2011-03-23, Last modification date: 2023-09-13)

Primary citation

Koh, Y.Y.,Wang, Y.,Qiu, C.,Opperman, L.,Gross, L.,Tanaka Hall, T.M.,Wickens, M.
Stacking interactions in PUF-RNA complexes.
Rna, 17:718-727, 2011

PubMed Abstract: Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to "target" versus "off-target" interactions, and thus be an important consideration in the design of proteins with new specificities.

PubMed: 21372189
DOI: 10.1261/rna.2540311

Experimental method

X-RAY DIFFRACTION (2.4 Å)