PMID: 19901328 , Related PDB ids: 3K5Q, 3K5Y, 3K5Z, 3K61, 3K62, 3K64

Authors:

Wang Y, Opperman L, Wickens M, Hall TM

Title:

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein.

Journal:

Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20186-91. Epub 2009 Nov 9.

Abstract:

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.