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Crystal structure of Prp5p reveals interdomain interactions that impact spliceosome assembly.

Zhang ZM, Yang F, Zhang J, Tang Q, Li J, Gu J, Zhou J, Xu YZ
Cell Rep 5 1269-78 (2013)
Cited: 18 times
EuropePMC logo PMID: 24290758

Abstract

The DEAD-box adenosine triphosphatase (ATPase) Prp5p facilitates U2 small nuclear ribonucleoprotein particle (snRNP) binding to the intron branch site region during spliceosome assembly. We present crystal structures of S. cerevisiae Prp5p alone and in complex with ADP at 2.12 Å and 1.95 Å resolution. The three-dimensional packing of Prp5p subdomains differs strikingly from that so far observed in other DEAD-box proteins: two RecA-like subdomains adopt an "open state" conformation stabilized by extensive interactions involving sequences that flank the two subdomains. This conformation is distinct from that required for ATP hydrolysis. Consistent with this, Prp5p mutations that destabilize interdomain interactions exhibited increased ATPase activity in vitro and inhibited splicing of suboptimal branch site substrates in vivo, whereas restoration of interdomain interactions reversed these effects. We conclude that the Prp5p open state conformation is biologically relevant and that disruption of the interdomain interaction facilitates a large-scale conformational change of Prp5p during U2 snRNP-branch site recognition.

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  1. SF3b1 mutations associated with myelodysplastic syndromes alter the fidelity of branchsite selection in yeast. Carrocci TJ, Zoerner DM, Paulson JC, Hoskins AA. Nucleic Acids Res. 45 4837-4852 (2017)
  2. Structural analysis of the spliceosomal RNA helicase Prp28 from the thermophilic eukaryote Chaetomium thermophilum. Tauchert MJ, Ficner R. Acta Crystallogr F Struct Biol Commun 72 409-416 (2016)
  3. RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis. Ngo TD, Partin AC, Nam Y. Cell Rep 29 4024-4035.e5 (2019)


Reviews citing this publication (6)

  1. Functions and regulation of the Brr2 RNA helicase during splicing. Absmeier E, Santos KF, Wahl MC. Cell Cycle 15 3362-3377 (2016)
  2. Unraveling the importance of the malaria parasite helicases. Tuteja R. FEBS J. 284 2592-2603 (2017)
  3. Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy. DeHaven AC, Norden IS, Hoskins AA. Wiley Interdiscip Rev RNA 7 683-701 (2016)
  4. Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Meiser N, Fuks C, Hengesbach M. Molecules 25 (2020)
  5. The organization and contribution of helicases to RNA splicing. De I, Schmitzová J, Pena V. Wiley Interdiscip Rev RNA 7 259-274 (2016)
  6. Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. van der Feltz C, Hoskins AA. Crit. Rev. Biochem. Mol. Biol. 54 443-465 (2019)

Articles citing this publication (9)

  1. A novel mechanism for Prp5 function in prespliceosome formation and proofreading the branch site sequence. Liang WW, Cheng SC. Genes Dev. 29 81-93 (2015)
  2. SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing. Tang Q, Rodriguez-Santiago S, Wang J, Pu J, Yuste A, Gupta V, Moldón A, Xu YZ, Query CC. Genes Dev. 30 2710-2723 (2016)
  3. Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Jacewicz A, Schwer B, Smith P, Shuman S. Nucleic Acids Res. 42 12885-12898 (2014)
  4. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3. Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA. J. Biol. Chem. 291 2412-2421 (2016)
  5. A novel endolysin disrupts Streptococcus suis with high efficiency. Ji W, Huang Q, Sun L, Wang H, Yan Y, Sun J. FEMS Microbiol. Lett. 362 fnv205 (2015)
  6. Error-Prone Splicing Controlled by the Ubiquitin Relative Hub1. Karaduman R, Chanarat S, Pfander B, Jentsch S. Mol. Cell 67 423-432.e4 (2017)
  7. Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly. Beier DH, Carrocci TJ, van der Feltz C, Tretbar US, Paulson JC, Grabowski N, Hoskins AA. Nucleic Acids Res. 47 10842-10851 (2019)
  8. Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities. Song QX, Liu NN, Liu ZX, Zhang YZ, Rety S, Hou XM, Xi XG. J Biol Chem 299 104592 (2023)
  9. Prp5-Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription. Shao W, Ding Z, Zheng ZZ, Shen JJ, Shen YX, Pu J, Fan YJ, Query CC, Xu YZ. Nucleic Acids Res 48 5799-5813 (2020)


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