Structural Insights into the Mechanism of the DEAH-box RNA Helicase Prp43

Overview

Journal Elife

Specialty Biology

Date 2017 Jan 17

PMID 28092261

Citations 50

Authors

Marcel J Tauchert

Jean-Baptiste Fourmann

Reinhard Luhrmann

Ralf Ficner

Affiliations

Soon will be listed here.

Abstract

The DEAH-box helicase Prp43 is a key player in pre-mRNA splicing as well as the maturation of rRNAs. The exact 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.

Citing Articles

Direct and Indirect Protein Interactions Link FUS Aggregation to Histone Post-Translational Modification Dysregulation and Growth Suppression in an ALS/FTD Yeast Model.

Bennett S, Cobos S, Fisher R, Son E, Frederic R, Segal R J Fungi (Basel). 2025; 11(1).

PMID: 39852477 PMC: 11766905. DOI: 10.3390/jof11010058.

An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly.

Portugal-Calisto D, Geiger A, Rabl J, Vadas O, Oborska-Oplova M, Mazur J Nat Commun. 2024; 15(1):10150.

PMID: 39578461 PMC: 11584650. DOI: 10.1038/s41467-024-54584-5.

Regulation and mechanisms of action of RNA helicases.

Lang N, Jagtap P, Hennig J RNA Biol. 2024; 21(1):24-38.

PMID: 39435974 PMC: 11498004. DOI: 10.1080/15476286.2024.2415801.

Unveiling the DHX15-G-patch interplay in retroviral RNA packaging.

Dostalkova A, Krizova I, Junkova P, Rackova J, Kapisheva M, Novotny R Proc Natl Acad Sci U S A. 2024; 121(40):e2407990121.

PMID: 39320912 PMC: 11459146. DOI: 10.1073/pnas.2407990121.

Mechanism for the initiation of spliceosome disassembly.

Vorlander M, Rothe P, Kleifeld J, Cormack E, Veleti L, Riabov-Bassat D Nature. 2024; 632(8024):443-450.

PMID: 38925148 PMC: 7616679. DOI: 10.1038/s41586-024-07741-1.

References

Tsai R, Tseng C, Lee P, Chen H, Fu R, Chang K . Dynamic interactions of Ntr1-Ntr2 with Prp43 and with U5 govern the recruitment of Prp43 to mediate spliceosome disassembly. Mol Cell Biol. 2007; 27(23):8027-37. PMC: 2169193. DOI: 10.1128/MCB.01213-07. View

Warkocki Z, Schneider C, Mozaffari-Jovin S, Schmitzova J, Hobartner C, Fabrizio P . The G-patch protein Spp2 couples the spliceosome-stimulated ATPase activity of the DEAH-box protein Prp2 to catalytic activation of the spliceosome. Genes Dev. 2015; 29(1):94-107. PMC: 4285774. DOI: 10.1101/gad.253070.114. View

Agarwal K, MIECH R, Parks Jr R . Guanylate kinases from human erythrocytes, hog brain, and rat liver. Methods Enzymol. 1978; 51:483-90. DOI: 10.1016/s0076-6879(78)51066-5. View

Christian H, Hofele R, Urlaub H, Ficner R . Insights into the activation of the helicase Prp43 by biochemical studies and structural mass spectrometry. Nucleic Acids Res. 2013; 42(2):1162-79. PMC: 3902948. DOI: 10.1093/nar/gkt985. View

Belon C, Frick D . Monitoring helicase activity with molecular beacons. Biotechniques. 2008; 45(4):433-40, 442. PMC: 2575809. DOI: 10.2144/000112834. View

Bohnsack M, Martin R, Granneman S, Ruprecht M, Schleiff E, Tollervey D . Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis. Mol Cell. 2009; 36(4):583-92. PMC: 2806949. DOI: 10.1016/j.molcel.2009.09.039. View

Fourmann J, Schmitzova J, Christian H, Urlaub H, Ficner R, Boon K . Dissection of the factor requirements for spliceosome disassembly and the elucidation of its dissociation products using a purified splicing system. Genes Dev. 2013; 27(4):413-28. PMC: 3589558. DOI: 10.1101/gad.207779.112. View

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

Pandit S, Lynn B, Rymond B . Inhibition of a spliceosome turnover pathway suppresses splicing defects. Proc Natl Acad Sci U S A. 2006; 103(37):13700-5. PMC: 1564266. DOI: 10.1073/pnas.0603188103. View

10.

Adams P, Afonine P, Bunkoczi G, Chen V, Davis I, Echols N . PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 2):213-21. PMC: 2815670. DOI: 10.1107/S0907444909052925. View

11.

. UniProt: a hub for protein information. Nucleic Acids Res. 2014; 43(Database issue):D204-12. PMC: 4384041. DOI: 10.1093/nar/gku989. View

12.

Singleton M, Dillingham M, Wigley D . Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem. 2007; 76:23-50. DOI: 10.1146/annurev.biochem.76.052305.115300. View

13.

Robert X, Gouet P . Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 2014; 42(Web Server issue):W320-4. PMC: 4086106. DOI: 10.1093/nar/gku316. View

14.

Fairman-Williams M, Guenther U, Jankowsky E . SF1 and SF2 helicases: family matters. Curr Opin Struct Biol. 2010; 20(3):313-24. PMC: 2916977. DOI: 10.1016/j.sbi.2010.03.011. View

15.

Schneider S, Schwer B . Functional domains of the yeast splicing factor Prp22p. J Biol Chem. 2001; 276(24):21184-91. DOI: 10.1074/jbc.M101964200. View

16.

Banroques J, Doere M, Dreyfus M, Linder P, Tanner N . Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1. J Mol Biol. 2009; 396(4):949-66. DOI: 10.1016/j.jmb.2009.12.025. View

17.

Fitzgerald M, Rawling D, Potapova O, Ren X, Kohlway A, Pyle A . Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding. Nucleic Acids Res. 2017; 45(3):1442-1454. PMC: 5388420. DOI: 10.1093/nar/gkw816. View

18.

Lebaron S, Papin C, Capeyrou R, Chen Y, Froment C, Monsarrat B . The ATPase and helicase activities of Prp43p are stimulated by the G-patch protein Pfa1p during yeast ribosome biogenesis. EMBO J. 2009; 28(24):3808-19. PMC: 2797057. DOI: 10.1038/emboj.2009.335. View

19.

Cordin O, Beggs J . RNA helicases in splicing. RNA Biol. 2012; 10(1):83-95. PMC: 3590240. DOI: 10.4161/rna.22547. View

20.

Ellman G . Tissue sulfhydryl groups. Arch Biochem Biophys. 1959; 82(1):70-7. DOI: 10.1016/0003-9861(59)90090-6. View