SNAP output for PDB entry 5ith [SNAP web server]

PDB-id

5ith; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein-DNA

Method

X-ray (2.31 Å)

Summary

Tia-1 rrm2 recognition of target oligonucleotide

Reference

Waris S, Garcia-Maurino SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Diaz-Moreno I, Wilce MCJ, Wilce JA (2017): "TIA-1 RRM23 binding and recognition of target oligonucleotides." Nucleic Acids Res., 45, 4944-4957. doi: 10.1093/nar/gkx102.

Abstract

TIA-1 (T-cell restricted intracellular antigen-1) is an RNA-binding protein involved in splicing and translational repression. It mainly interacts with RNA via its second and third RNA recognition motifs (RRMs), with specificity for U-rich sequences directed by RRM2. It has recently been shown that RRM3 also contributes to binding, with preferential binding for C-rich sequences. Here we designed UC-rich and CU-rich 10-nt sequences for engagement of both RRM2 and RRM3 and demonstrated that the TIA-1 RRM23 construct preferentially binds the UC-rich RNA ligand (5΄-UUUUUACUCC-3΄). Interestingly, this binding depends on the presence of Lys274 that is C-terminal to RRM3 and binding to equivalent DNA sequences occurs with similar affinity. Small-angle X-ray scattering was used to demonstrate that, upon complex formation with target RNA or DNA, TIA-1 RRM23 adopts a compact structure, showing that both RRMs engage with the target 10-nt sequences to form the complex. We also report the crystal structure of TIA-1 RRM2 in complex with DNA to 2.3 Å resolution providing the first atomic resolution structure of any TIA protein RRM in complex with oligonucleotide. Together our data support a specific mode of TIA-1 RRM23 interaction with target oligonucleotides consistent with the role of TIA-1 in binding RNA to regulate gene expression.