Essential Protein Factors in pre-mRNA splicing : A Structural Study by Nuclear Magnetic Resonance Spectroscopy

This thesis describes two novel three-dimensional structures and the functional characterization of proteins that play important roles in eukaryotic RNA splicing. These results are discussed in Chapters 1 and 2, while biomolecular NMR techniques that were employed for the structure determination are outlined in Chapter 3. Materials and methods are described in Chapter 4. Chapter 1 presents the solution structure of the Tudor domain of the human Survival of Motor Neuron (SMN) protein and its molecular interaction with the spliceosomal Sm proteins. Sm proteins are common components of small nuclear ribonucleoprotein particles (snRNPs), which are assembled by a protein complex that contains SMN. The structure of the SMN Tudor domain exhibits a five stranded ?-barrel, which resembles the fold of Sm proteins. The Tudor domain of SMN binds to arginine and glycine-rich C-terminal regions of Sm proteins, where it specifically recognizes symmetrically di-methylated arginine residues. The E134K mutant Tudor domain, which corresponds to a human mutation associated with Spinal Muscular Atrophy (SMA), is structurally intact but fails to interact with Sm proteins. This provides an explanation for a molecular defect underlying SMA. In Chapter 2, the structural basis for the molecular recognition between the essential splicing factors SF1 and U2 auxiliary factor 2 (U2AF) is provided. This interaction involves the third RNA recognition motif (RRM3) of the large subunit of U2AF (U2AF65) and the N-terminal 25 residues of SF1. The structure of RRM3 exhibits the classical RNP-type fold, but contains an additional C-terminal helix. SF1 is bound by the helical surface of RRM3, opposite of the canonical RNA binding site. The molecular recognition involves insertion of a conserved tryptophan of SF1 into a hydrophobic binding pocket of RRM3. This interaction is complemented by electrostatic contacts that are mediated by acidic residues of RRM3 and basic amino acids of SF1. Surprisingly, the molecular interface is highly similar to that between the large (U2AF65) and small (U2AF35) subunits of U2AF. This RRM-mediated protein interaction provides an example of how conserved structural folds have evolved different molecular functions