Research Article: Crystal structure of the spliceosomal DEAH-box ATPase Prp2

Date Published: July 01, 2018

Publisher: International Union of Crystallography

Author(s): Andreas Schmitt, Florian Hamann, Piotr Neumann, Ralf Ficner.


The DEAH-box ATPase Prp2 is a key player during pre-mRNA splicing. Here, the first four crystal structures of this spliceosomal factor are reported in two different states, and the flexibility of its C-terminal domains and a previously undescribed ADP conformation are reported.

Partial Text

In eukaryotic cells, precursor messenger RNAs (pre-mRNAs) may contain noncoding intervening sequences (introns) that have to be removed by splicing prior to nuclear export and translation of the mRNAs. The process of pre-mRNA splicing is carried out by a highly dynamic multi-megadalton ribo­nucleoprotein (RNP) complex, the spliceosome, which catalyzes two sequential transesterification reactions (Will & Lührmann, 2011 ▸; Hoskins & Moore, 2012 ▸; Matera & Wang, 2014 ▸). For each intron to be excised, the spliceosome assembles stepwise onto the pre-mRNA from five small nuclear ribonucleoprotein particles (snRNPs), named U1, U2, U4/U6 and U5, and a large number of non-snRNP proteins (Wahl et al., 2009 ▸). Briefly, the assembly starts with the U1 snRNP binding to the 5′ splice site of the pre-mRNA and the U2 snRNP interacting with the branch-point sequence (BPS), resulting in the formation of the spliceosomal A complex. Subsequently, the pre-assembled tri-snRNP consisting of the U4/U6 and U5 snRNPs is recruited to the spliceosome, leading to the formation of the catalytically inactive Bact complex. In the subsequent step of the splicing cycle, the catalytically active B* complex is formed which facilitates the first transesterification reaction. After this, complex C is made by further remodelling and the second transesterification reaction takes place. Finally, the spliceosome is disassembled, leading to release of the spliced mRNA and the intron lariat.

Here, we report the first crystal structures of Prp2 in two different functional states (nucleotide-free and ADP-bound). The atomic models of both functional states share a very similar conformation and their overall structures strongly resemble the structure of the closely related DEAH-box helicase Prp43 (Fig. 2 ▸). However, despite these structural similarities, Prp2 and Prp43 differ significantly in their function. In contrast to all other spliceosomal DEAH-box proteins, no helicase activity has been observed for Prp2 in vitro (Warkocki et al., 2015 ▸; Bao et al., 2017 ▸). This atypical lack of helicase activity appears to be consistent with the function of Prp2 as deduced from the recently determined cryo-EM structures of the Bact complex (Rauhut et al., 2016 ▸; Yan et al., 2016 ▸). Prp2 is located on the periphery of the Bact spliceosome, contacting the outer side of the Hsh155 HEAT repeats, and therefore Prp2 is rather distant from the 5′ splice site and the branch-point adenosine (Supplementary Fig. S4). This is in agreement with previous biochemical data showing that Prp2 binds to the single-stranded intron ∼30 nt downstream of the branch-point site (Liu & Cheng, 2012 ▸; Warkocki et al., 2015 ▸). All data to date suggest that Prp2 does not act as a helicase by unwinding double-stranded RNAs, but rather functions as an RNA-dependent RNPase. The analysis of different functional states of Prp2 might provide insight into the peculiar manner of function of this spliceosomal DEAH-box helicase.

The following references are cited in the Supporting Information for this article: Fica et al. (2017 ▸) and Liu et al. (2017 ▸).




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