An RBD that does not bind RNA: NMR secondary structure determination and biochemical properties of the C-terminal RNA binding domain from the human U1A protein

We have obtained backbone ¹H, ¹⁵N, and ¹³C assignments and determined the secondary structure and folding topology of the C-terminal RNA-binding domain (RBD) of the human U1A protein. The secondary structure derived from NOE data is in excellent agreement with the predicted structure from the ¹H and ¹³C chemical shift indices. This 88 amino acid domain exhibits a βαβ-βαβ folding pattern, with conserved RNP1 and RNP2 sequences located in two adjacent strands of a four-strand antiparallel β-sheet. This global folding pattern is typical of this class of RNA binding proteins. Although this domain contains residues that are conserved in all RBDs, its RNA binding properties are very unusual. RNA binding studies show that this domain does not bind U1, U2 or U5 snRNA, an RNA hairpin, rA₁₆, rU₁₆, rC₁₆ or rA₃U₃GUA₄, nor does it show significant association to populations of random sequence RNAs.