Crystal structures of U6 snRNA-specific terminal uridylyltransferase

Seisuke Yamashita,Kozo Tomita,Takashi Nagaike,Yuko Takagi

doi:10.1038/ncomms15788

Seisuke Yamashita, Kozo Tomita + Show 2 more

Open Access

https://doi.org/10.1038/ncomms15788

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Abstract

The terminal uridylyltransferase, TUT1, builds or repairs the 3′-oligo-uridylylated tail of U6 snRNA. The 3′-oligo-uridylylated tail is the Lsm-binding site for U4/U6 di-snRNP formation and U6 snRNA recycling for pre-mRNA splicing. Here, we report crystallographic and biochemical analyses of human TUT1, which revealed the mechanisms for the specific uridylylation of the 3′-end of U6 snRNA by TUT1. The O2 and O4 atoms of the UTP base form hydrogen bonds with the conserved His and Asn in the catalytic pocket, respectively, and TUT1 preferentially incorporates UMP onto the 3′-end of RNAs. TUT1 recognizes the entire U6 snRNA molecule by its catalytic domains, N-terminal RNA-recognition motifs and a previously unidentified C-terminal RNA-binding domain. Each domain recognizes specific regions within U6 snRNA, and the recognition is coupled with the domain movements and U6 snRNA structural changes. Hence, TUT1 functions as the U6 snRNA-specific terminal uridylyltransferase required for pre-mRNA splicing.

Highlights

The terminal uridylyltransferase, TUT1, builds or repairs the 30-oligo-uridylylated tail of U6 snRNA
The structure of the TUT1 nucleotide-binding pocket is suitable for interactions with UTP, through specific hydrogen bonds between the uracil base and the conserved His and Asn residues in the catalytic pocket (Fig. 2b)
The C-terminal domain is topologically homologous to the Microtubule Affinity-Regulating Kinase 3 (MARK-3) KA-1 domain, which interacts with phospholipids[26]

Summary

Introduction

The terminal uridylyltransferase, TUT1, builds or repairs the 30-oligo-uridylylated tail of U6 snRNA. The 30-oligo-uridylylated tail is the Lsm-binding site for U4/U6 di-snRNP formation and U6 snRNA recycling for pre-mRNA splicing. The oligo-uridylylated tail is trimmed by a 30-50 exonuclease, Mpn[1] (Usb1)[14,15,16], and the 30 end of the resultant mature U6 snRNA has five uridines with a 20,30-cyclic phosphate (4p). The oligo-uridylylated tail of the U6 snRNA is the binding site for the Lsm[2,3,4,5,6,7,8] ring protein complexes[4,17], for the annealing of the U6 and U4 snRNAs to form the di-U4/U6 snRNP, and for the recycling of the U6 snRNA after the splicing reaction, together with p110 Crystallographic and biochemical studies of TUT1 revealed the molecular mechanism underlying the specific oligo-uridylylation of the 30-end of U6 snRNA by TUT1

Methods

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Conclusion