Structural insights into the mechanism of the DEAH-box RNA helicase Prp43

Abstract
Data availability
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Abstract

The DEAH-box helicase Prp43 is a key player in pre-mRNA splicing as well as the maturation of rRNAs. The exact modus operandi of Prp43 and of all other spliceosomal DEAH-box RNA helicases is still elusive. Here, we report crystal structures of Prp43 complexes in different functional states and the analysis of structure-based mutants providing insights into the unwinding and loading mechanism of RNAs. The Prp43•ATP-analog•RNA complex shows the localization of the RNA inside a tunnel formed by the two RecA-like and C-terminal domains. In the ATP-bound state this tunnel can be transformed into a groove prone for RNA binding by large rearrangements of the C-terminal domains. Several conformational changes between the ATP- and ADP-bound states explain the coupling of ATP hydrolysis to RNA translocation, mainly mediated by a β-turn of the RecA1 domain containing the newly identified RF motif. This mechanism is clearly different to those of other RNA helicases.

Data availability

The following data sets were generated

1. Tauchert MJ
2. Ficner R
(2016) Crystal structure of the Prp43-ADP-BeF3-U7-RNA complex
Publicly available at the RCSB Protein Data Bank (accession no: 5LTA).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5LTA
1. Tauchert MJ
2. Ficner R
(2016) Crystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic space group)
Publicly available at the RCSB Protein Data Bank (accession no: 5ltj).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5LTJ
1. Tauchert MJ
2. Ficner R
(2016) Crystal structure of the Prp43-ADP-BeF3 complex (in hexagonal space group)
Publicly available at the RCSB Protein Data Bank (accession no: 5LTK).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5LTK

The following previously published data sets were used

1. Tauchert MJ
2. Ficner R
(2016) Crystal structure of the RNA-helicase Prp43 from Chaetomium thermophilum bound to ADP
Publicly available at the RCSB Protein Data Bank (accession no: 5D0U).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5D0U
1. Prabu JR
2. Conti E
(2015) Structure of MLE RNA ADP AlF4 complex
Publicly available at the RCSB Protein Data Bank (accession no: 5AOR).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5AOR
1. Appleby TC
2. Somoza JR
(2011) Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV
Publicly available at the RCSB Protein Data Bank (accession no: 3O8R).

http://www.rcsb.org/pdb/explore/explore.do?structureId=3O8R

Article and author information

Author details

Marcel J Tauchert

Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.
Jean-Baptiste Fourmann

Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.
Reinhard Lührmann

Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6403-4432
Ralf Ficner

Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany

For correspondence
rficner@uni-goettingen.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1739-6086

Funding

Deutsche Forschungsgemeinschaft ((SFB860 TPA2))

Ralf Ficner

Deutsche Forschungsgemeinschaft ((SFB860 TPA1))

Reinhard Lührmann

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.