Crystal structure of Prp8 reveals active site cavity of the spliceosome (original) (raw)
Wahl, M. C., Will, C. L. & Lührmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell136, 701–718 (2009) ArticleCAS Google Scholar
Wassarman, D. A. & Steitz, J. A. Interactions of small nuclear RNA’s with precursor messenger RNA during in vitro splicing. Science257, 1918–1925 (1992) ArticleADSCAS Google Scholar
Madhani, H. D. & Guthrie, C. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell71, 803–817 (1992) ArticleCAS Google Scholar
Kandels-Lewis, S. & Seraphin, B. Involvement of U6 snRNA in 5′ splice site selection. Science262, 2035–2039 (1993) ArticleADSCAS Google Scholar
Lesser, C. F. & Guthrie, C. Mutations in U6 snRNA that alter splice site specificity: Implications for the active site. Science262, 1982–1988 (1993) ArticleADSCAS Google Scholar
Sun, J. S. & Manley, J. L. A novel U2–U6 snRNA structure is necessary for mammalian mRNA splicing. Genes Dev.9, 843–854 (1995) ArticleCAS Google Scholar
Yean, S.-L., Wuenschell, G., Termini, J. & Lin, R. J. Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Nature408, 881–884 (2000) ArticleADSCAS Google Scholar
Steitz, T. A. & Steitz, J. A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA90, 6498–6502 (1993) ArticleADSCAS Google Scholar
Newman, A. J. & Norman, C. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell68, 743–754 (1992) ArticleCAS Google Scholar
Sontheimer, E. J. & Steitz, J. A. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science262, 1989–1996 (1993) ArticleADSCAS Google Scholar
O'Keefe, R. T., Norman, C. & Newman, A. J. The invariant U5 snRNA loop 1 sequence is dispensable for the first catalytic step of pre-mRNA splicing in yeast. Cell86, 679–689 (1996) ArticleCAS Google Scholar
Achsel, T., Ahrens, K., Brahms, H., Teigelkamp, S. & Lührmann, R. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. Mol. Cell. Biol.18, 6756–6766 (1998) ArticleCAS Google Scholar
Bartels, C., Urlaub, H., Lührmann, R. & Fabrizio, P. Mutagenesis suggests several roles of Snu114p in pre-mRNA splicing. J. Biol. Chem.278, 28324–28334 (2003) ArticleCAS Google Scholar
Small, E. C., Leggett, S. R., Winans, A. A. & Staley, J. P. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol. Cell23, 389–399 (2006) ArticleCAS Google Scholar
Teigelkamp, S., Newman, A. J. & Beggs, J. D. Extensive interactions of PRP8 protein with the 5′ and 3′ splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J.14, 2602–2612 (1995) ArticleCAS Google Scholar
Dix, I., Russell, C. S., O’Keefe, R. T., Newman, A. J. & Beggs, J. D. Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae. RNA4, 1239–1250 (1998) ArticleCAS Google Scholar
Vidal, V. P., Verdone, L., Mayes, A. E. & Beggs, J. D. Characterization of U6 snRNA-protein interactions. RNA5, 1470–1481 (1999) ArticleCAS Google Scholar
Reyes, J. L., Gustafson, E. H., Luo, H. R., Moore, M. J. & Konarska, M. M. The C-terminal region of hPrp8 interacts with the conserved GU dinucleotide at the 5′ splice site. RNA5, 167–179 (1999) ArticleCAS Google Scholar
MacMillan, A. M. et al. Dynamic association of proteins with the pre-mRNA branch region. Genes Dev.8, 3008–3020 (1994) ArticleCAS Google Scholar
Turner, I. A., Norman, C. M., Churcher, M. J. & Newman, A. J. Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome. RNA12, 375–386 (2006) ArticleCAS Google Scholar
Grainger, R. J. & Beggs, J. D. Prp8 protein: at the heart of the spliceosome. RNA11, 533–557 (2005) ArticleCAS Google Scholar
Pena, V., Rozov, A., Fabrizio, P., Lührmann, R. & Wahl, M. C. Structure and function of an RNase H domain at the heart of the spliceosome. EMBO J.27, 2929–2940 (2008) ArticleCAS Google Scholar
Ritchie, D. B. et al. Structural elucidation of a PRP8 core domain from the heart of the spliceosome. Nature Struct. Mol. Biol.15, 1199–1205 (2008) ArticleCAS Google Scholar
Yang, K., Zhang, L., Xu, T., Heroux, A. & Zhao, R. Crystal structure of the β-finger domain of Prp8 reveals analogy to ribosomal proteins. Proc. Natl Acad. Sci. USA105, 13817–13822 (2008) ArticleADSCAS Google Scholar
Pena, V., Liu, S., Bujnicki, J. M., Lührmann, R. & Wahl, M. C. Structure of a multipartite protein-protein interaction domain in splicing factor Prp8 and its link to Retinitis pigmentosa. Mol. Cell25, 615–624 (2007) ArticleCAS Google Scholar
Zhang, L. et al. Crystal structure of the C-terminal domain of splicing factor Prp8 carrying retinitis pigmentosa mutants. Protein Sci.16, 1024–1031 (2007) ArticleCAS Google Scholar
Dlakić, M. & Mushegian, A. Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase. RNA17, 799–808 (2011) Article Google Scholar
Boon, K. L. et al. Prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast. Nature Struct. Mol. Biol.14, 1077–1083 (2007) ArticleCAS Google Scholar
Weber, G. et al. Mechanism for Aar2p function as a U5 snRNP assembly factor. Genes Dev.25, 1601–1612 (2011) ArticleCAS Google Scholar
Joyce, C. M. & Steitz, T. A. Function and structure relationships in DNA polymerase. Annu. Rev. Biochem.63, 777–822 (1994) ArticleCAS Google Scholar
Dias, A. et al. The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. Nature458, 914–918 (2009) ArticleADSCAS Google Scholar
Yuan, P. et al. Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site. Nature458, 909–913 (2009) ArticleADSCAS Google Scholar
Wyatt, J. R., Sontheimer, E. J. & Steitz, J. A. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes Dev.6, 2542–2553 (1992) ArticleCAS Google Scholar
Urlaub, H., Hartmuth, K., Kostka, S., Grelle, G. & Lührmann, R. A general approach for identification of RNA-protein cross-linking sites within native human spliceosomal small nuclear ribonucleoproteins (snRNPs). J. Biol. Chem.275, 41458–41468 (2000) ArticleCAS Google Scholar
Query, C. C. & Konarska, M. M. Suppression of multiple substrate mutations by spliceosomal prp8 alleles suggests functional correlations with ribosomal ambiguity mutants. Mol. Cell14, 343–354 (2004) ArticleCAS Google Scholar
Umen, J. G. & Guthrie, C. Mutagenesis of the yeast gene PRP8 reveals domains governing the specificity and fidelity of 3′ splice site selection. Genetics143, 723–739 (1996) CASPubMedPubMed Central Google Scholar
Kuhn, A. N. & Brow, D. A. Suppressors of a cold-sensitive mutation in yeast U4 RNA define five domains in the splicing factor Prp8 that influence spliceosome activation. Genetics155, 1667–1682 (2000) CASPubMedPubMed Central Google Scholar
Kuhn, A. N., Reichl, E. M. & Brow, D. A. Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation. Proc. Natl Acad. Sci. USA99, 9145–9149 (2002) ArticleADSCAS Google Scholar
Sharp, P. A. On the origin of RNA splicing and introns. Cell42, 397–400 (1985) ArticleCAS Google Scholar
Cech, T. R. The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell44, 207–210 (1986) ArticleCAS Google Scholar
Michel, F., Umesono, K. & Ozeki, H. Comparative and functional anatomy of group II catalytic introns—a review. Gene82, 5–30 (1989) ArticleCAS Google Scholar
Lambowitz, A. M. & Zimmerly, S. Mobile group II introns. Annu. Rev. Genet.38, 1–35 (2004) ArticleCAS Google Scholar
Pyle, A. M. & Lambowitz, A. M. in The RNA World 3rd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F. ) 469–505 (Cold Spring Harbor Laboratory Press, 2006) Google Scholar
Qui, Y.-L. & Palmer, J. D. Many different origins of trans splicing in a plant mitochondrial group II intron. J. Mol. Evol.59, 80–89 (2004) Google Scholar
Toor, N. et al. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA16, 57–69 (2010) ArticleCAS Google Scholar
Marcia, M. & Pyle, A. M. Visualizing group II intron catalysis through the stages of splicing. Cell151, 497–507 (2012) ArticleCAS Google Scholar
Matsuura, M., Noah, J. W. & Lambowitz, A. M. Mechanism of maturase-promoted group II intron splicing. EMBO J.20, 7259–7270 (2001) ArticleCAS Google Scholar
Rambo, R. P. & Doudna, J. A. Assembly of an active group II intron-maturase complex by protein dimerization. Biochemistry43, 6486–6497 (2004) ArticleCAS Google Scholar
Gu, S. Q. et al. Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase. RNA16, 732–747 (2010) ArticleCAS Google Scholar
Wagenbach, M. et al. Synthesis of wild type and mutant human hemoglobins in Saccharomyces cerevisiae. Biotechnology (N Y)9, 57–61 (1991) CAS Google Scholar
Christianson, T. W., Sikorski, R. S., Dante, M., Shero, J. H. & Hieter, P. Multifunctional yeast high-copy-number shuttle vectors. Gene110, 119–122 (1992) ArticleCAS Google Scholar
Leslie, A. G. W. & Powell, H. R. Processing diffraction data with Mosflm. Evolv. Methods Macromol. Crystallograph.245, 41–51 (2007) Article Google Scholar
Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D62, 72–82 (2006) Article Google Scholar
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr.40, 658–674 (2007) ArticleCAS Google Scholar
Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D66, 22–25 (2010) ArticleCAS Google Scholar
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240–255 (1997) ArticleCAS Google Scholar
Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D66, 479–485 (2010) ArticleCAS Google Scholar
Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nature Protocols3, 1171–1179 (2008) ArticleCAS Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D60, 2126–2132 (2004) Article Google Scholar
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D66, 12–21 (2010) ArticleCAS Google Scholar
Krissinel, E. & Henrick, K. Secondary-structure matching (PDBeFold), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D60, 2256–2268 (2004) ArticleCAS Google Scholar
Holm, L. & Park, J. DaliLite workbench for protein structure comparison. Bioinformatics16, 566–567 (2000) ArticleCAS Google Scholar
Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA98, 10037–10041 (2001) ArticleADSCAS Google Scholar
Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res.38, 529–533 (2010) Article Google Scholar
Larkin, M. A. et al. ClustalW and ClustalX version 2. Bioinformatics23, 2947–2948 (2007) ArticleCAS Google Scholar
Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers22, 2577–2637 (1983) ArticleCAS Google Scholar
Heinig, M. & Frishman, D. STRIDE: a Web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res.32, W500–W502 (2004) ArticleCAS Google Scholar
Sikorski, R. S. & Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics122, 19–27 (1989) CASPubMedPubMed Central Google Scholar