Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0

Heterogeneous nuclear ribonucleoprotein (hnRNP) DO has two ribonucleoprotei n (RNP)-type RNA-binding domains (RBDs), each of which can bind solely to t he UUAG sequence specifically. The structure of the N-terminal RED (RBD1) d etermined by NMR is presented here. It folds into a compact alpha beta stru cture comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of the RNP-type RBDs. Special struc tural features of RBD1 include N-capping boxes for both alpha-helices, a be ta-bulge in the second beta-strand, and an additional short antiparallel be ta-sheet coupled with a beta-turn-like structure in a loop. Two hydrogen bo nds which restrict the positions of loops were identified. Backbone resonan ce assignments for RBD1 complexed with r(UUAGGG) revealed that the overall folding is maintained in the complex. The candidate residues involved in th e interactions with RNA were identified by chemical shift perturbation anal ysis. They are located in the central and peripheral regions of the RNA-bin ding surface composed of the four-stranded beta-sheet, loops, and the C-ter minal region. It is suggested that non-specific interactions with RNA are p erformed by the residues in the central region of the RNA-binding surface, while specific interactions are performed by those in the peripheral region s. It was also found that RBD1 has the ability to inhibit the formation of the quadruplex structure. (C) 1999 Academic Press.