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EMBO J. Jul 17, 1995; 14(14): 3563–3571.
PMCID: PMC394424

NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5.

Abstract

The double-stranded RNA binding domain (dsRBD) is an approximately 65 amino acid motif that is found in a variety of proteins that interact with double-stranded (ds) RNA, such as Escherichia coli RNase III and the dsRNA-dependent kinase, PKR. Drosophila staufen protein contains five copies of this motif, and the third of these binds dsRNA in vitro. Using multinuclear/multidimensional NMR methods, we have determined that staufen dsRBD3 forms a compact protein domain with an alpha-beta-beta-beta-alpha structure in which the two alpha-helices lie on one face of a three-stranded anti-parallel beta-sheet. This structure is very similar to that of the N-terminal domain of a prokaryotic ribosomal protein S5. Furthermore, the consensus derived from all known S5p family sequences shares several conserved residues with the dsRBD consensus sequence, indicating that the two domains share a common evolutionary origin. Using in vitro mutagenesis, we have identified several surface residues which are important for the RNA binding of the dsRBD, and these all lie on the same side of the domain. Two residues that are essential for RNA binding, F32 and K50, are also conserved in the S5 protein family, suggesting that the two domains interact with RNA in a similar way.

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These references are in PubMed. This may not be the complete list of references from this article.
  • Akusjärvi G, Mathews MB, Andersson P, Vennström B, Pettersson U. Structure of genes for virus-associated RNAI and RNAII of adenovirus type 2. Proc Natl Acad Sci U S A. 1980 May;77(5):2424–2428. [PMC free article] [PubMed]
  • Alden CJ, Kim SH. Solvent-accessible surfaces of nucleic acids. J Mol Biol. 1979 Aug 15;132(3):411–434. [PubMed]
  • All-Robyn JA, Brown N, Otaka E, Liebman SW. Sequence and functional similarity between a yeast ribosomal protein and the Escherichia coli S5 ram protein. Mol Cell Biol. 1990 Dec;10(12):6544–6553. [PMC free article] [PubMed]
  • Bandziulis RJ, Swanson MS, Dreyfuss G. RNA-binding proteins as developmental regulators. Genes Dev. 1989 Apr;3(4):431–437. [PubMed]
  • Bass BL, Weintraub H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell. 1988 Dec 23;55(6):1089–1098. [PubMed]
  • Biou V, Yaremchuk A, Tukalo M, Cusack S. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 1994 Mar 11;263(5152):1404–1410. [PubMed]
  • Birney E, Kumar S, Krainer AR. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res. 1993 Dec 25;21(25):5803–5816. [PMC free article] [PubMed]
  • Brimacombe R. RNA-protein interactions in the Escherichia coli ribosome. Biochimie. 1991 Jul-Aug;73(7-8):927–936. [PubMed]
  • Burd CG, Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science. 1994 Jul 29;265(5172):615–621. [PubMed]
  • Castiglone Morelli MA, Stier G, Gibson T, Joseph C, Musco G, Pastore A, Travè G. The KH module has an alpha beta fold. FEBS Lett. 1995 Jan 23;358(2):193–198. [PubMed]
  • Dock-Bregeon AC, Chevrier B, Podjarny A, Johnson J, de Bear JS, Gough GR, Gilham PT, Moras D. Crystallographic structure of an RNA helix: [U(UA)6A]2. J Mol Biol. 1989 Oct 5;209(3):459–474. [PubMed]
  • Ferrandon D, Elphick L, Nüsslein-Volhard C, St Johnston D. Staufen protein associates with the 3'UTR of bicoid mRNA to form particles that move in a microtubule-dependent manner. Cell. 1994 Dec 30;79(7):1221–1232. [PubMed]
  • Gibson TJ, Thompson JD. Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases. Nucleic Acids Res. 1994 Jul 11;22(13):2552–2556. [PMC free article] [PubMed]
  • Gibson TJ, Thompson JD, Heringa J. The KH domain occurs in a diverse set of RNA-binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid. FEBS Lett. 1993 Jun 21;324(3):361–366. [PubMed]
  • Golden BL, Hoffman DW, Ramakrishnan V, White SW. Ribosomal protein S17: characterization of the three-dimensional structure by 1H and 15N NMR. Biochemistry. 1993 Nov 30;32(47):12812–12820. [PubMed]
  • Good L, Nazar RN. An improved thermal cycle for two-step PCR-based targeted mutagenesis. Nucleic Acids Res. 1992 Sep 25;20(18):4934–4934. [PMC free article] [PubMed]
  • Green SR, Mathews MB. Two RNA-binding motifs in the double-stranded RNA-activated protein kinase, DAI. Genes Dev. 1992 Dec;6(12B):2478–2490. [PubMed]
  • Green SR, Manche L, Mathews MB. Two functionally distinct RNA-binding motifs in the regulatory domain of the protein kinase DAI. Mol Cell Biol. 1995 Jan;15(1):358–364. [PMC free article] [PubMed]
  • Hoffman DW, Query CC, Golden BL, White SW, Keene JD. RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2495–2499. [PMC free article] [PubMed]
  • Kharrat A, Macias MJ, Gibson TJ, Nilges M, Pastore A. Structure of the dsRNA binding domain of E. coli RNase III. EMBO J. 1995 Jul 17;14(14):3572–3584. [PMC free article] [PubMed]
  • Kim JL, Burley SK. 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol. 1994 Sep;1(9):638–653. [PubMed]
  • Kim U, Wang Y, Sanford T, Zeng Y, Nishikura K. Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11457–11461. [PMC free article] [PubMed]
  • Ladomery M, Sommerville J. Binding of Y-box proteins to RNA: involvement of different protein domains. Nucleic Acids Res. 1994 Dec 25;22(25):5582–5589. [PMC free article] [PubMed]
  • Lindahl M, Svensson LA, Liljas A, Sedelnikova SE, Eliseikina IA, Fomenkova NP, Nevskaya N, Nikonov SV, Garber MB, Muranova TA, et al. Crystal structure of the ribosomal protein S6 from Thermus thermophilus. EMBO J. 1994 Mar 15;13(6):1249–1254. [PMC free article] [PubMed]
  • Louie GV, Brownlie PD, Lambert R, Cooper JB, Blundell TL, Wood SP, Warren MJ, Woodcock SC, Jordan PM. Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site. Nature. 1992 Sep 3;359(6390):33–39. [PubMed]
  • Manche L, Green SR, Schmedt C, Mathews MB. Interactions between double-stranded RNA regulators and the protein kinase DAI. Mol Cell Biol. 1992 Nov;12(11):5238–5248. [PMC free article] [PubMed]
  • March PE, Ahnn J, Inouye M. The DNA sequence of the gene (rnc) encoding ribonuclease III of Escherichia coli. Nucleic Acids Res. 1985 Jul 11;13(13):4677–4685. [PMC free article] [PubMed]
  • Mattaj IW. RNA recognition: a family matter? Cell. 1993 Jun 4;73(5):837–840. [PubMed]
  • McMillan NA, Carpick BW, Hollis B, Toone WM, Zamanian-Daryoush M, Williams BR. Mutational analysis of the double-stranded RNA (dsRNA) binding domain of the dsRNA-activated protein kinase, PKR. J Biol Chem. 1995 Feb 10;270(6):2601–2606. [PubMed]
  • Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BR, Hovanessian AG. Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon. Cell. 1990 Jul 27;62(2):379–390. [PubMed]
  • Moras D, Poterszman A. RNA-protein interactions. Diverse modes of recognition. Curr Biol. 1995 Mar 1;5(3):249–251. [PubMed]
  • Murray MT. Nucleic acid-binding properties of the Xenopus oocyte Y box protein mRNP3+4. Biochemistry. 1994 Nov 22;33(46):13910–13917. [PubMed]
  • Murzin AG. A ribosomal protein module in EF-G and DNA gyrase. Nat Struct Biol. 1995 Jan;2(1):25–26. [PubMed]
  • Nagai K, Oubridge C, Jessen TH, Li J, Evans PR. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature. 1990 Dec 6;348(6301):515–520. [PubMed]
  • Neri D, Szyperski T, Otting G, Senn H, Wüthrich K. Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry. 1989 Sep 19;28(19):7510–7516. [PubMed]
  • Newkirk K, Feng W, Jiang W, Tejero R, Emerson SD, Inouye M, Montelione GT. Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5114–5118. [PMC free article] [PubMed]
  • O'Connell MA, Krause S, Higuchi M, Hsuan JJ, Totty NF, Jenny A, Keller W. Cloning of cDNAs encoding mammalian double-stranded RNA-specific adenosine deaminase. Mol Cell Biol. 1995 Mar;15(3):1389–1397. [PMC free article] [PubMed]
  • Oubridge C, Ito N, Evans PR, Teo CH, Nagai K. Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 1994 Dec 1;372(6505):432–438. [PubMed]
  • Picard V, Ersdal-Badju E, Lu A, Bock SC. A rapid and efficient one-tube PCR-based mutagenesis technique using Pfu DNA polymerase. Nucleic Acids Res. 1994 Jul 11;22(13):2587–2591. [PMC free article] [PubMed]
  • Polson AG, Bass BL. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 1994 Dec 1;13(23):5701–5711. [PMC free article] [PubMed]
  • Ramakrishnan V, White SW. The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature. 1992 Aug 27;358(6389):768–771. [PubMed]
  • Rinke-Appel J, Jünke N, Stade K, Brimacombe R. The path of mRNA through the Escherichia coli ribosome; site-directed cross-linking of mRNA analogues carrying a photo-reactive label at various points 3' to the decoding site. EMBO J. 1991 Aug;10(8):2195–2202. [PMC free article] [PubMed]
  • Robertson HD, Webster RE, Zinder ND. Purification and properties of ribonuclease III from Escherichia coli. J Biol Chem. 1968 Jan 10;243(1):82–91. [PubMed]
  • Schindelin H, Marahiel MA, Heinemann U. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature. 1993 Jul 8;364(6433):164–168. [PubMed]
  • Schindelin H, Jiang W, Inouye M, Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5119–5123. [PMC free article] [PubMed]
  • Schnuchel A, Wiltscheck R, Czisch M, Herrler M, Willimsky G, Graumann P, Marahiel MA, Holak TA. Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature. 1993 Jul 8;364(6433):169–171. [PubMed]
  • Schweisguth DC, Chelladurai BS, Nicholson AW, Moore PB. Structural characterization of a ribonuclease III processing signal. Nucleic Acids Res. 1994 Feb 25;22(4):604–612. [PMC free article] [PubMed]
  • Siomi H, Matunis MJ, Michael WM, Dreyfuss G. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res. 1993 Mar 11;21(5):1193–1198. [PMC free article] [PubMed]
  • Siomi H, Choi M, Siomi MC, Nussbaum RL, Dreyfuss G. Essential role for KH domains in RNA binding: impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome. Cell. 1994 Apr 8;77(1):33–39. [PubMed]
  • St Johnston D, Driever W, Berleth T, Richstein S, Nüsslein-Volhard C. Multiple steps in the localization of bicoid RNA to the anterior pole of the Drosophila oocyte. Development. 1989;107 (Suppl):13–19. [PubMed]
  • St Johnston D, Beuchle D, Nüsslein-Volhard C. Staufen, a gene required to localize maternal RNAs in the Drosophila egg. Cell. 1991 Jul 12;66(1):51–63. [PubMed]
  • St Johnston D, Brown NH, Gall JG, Jantsch M. A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10979–10983. [PMC free article] [PubMed]
  • Stern S, Powers T, Changchien LM, Noller HF. Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA. J Mol Biol. 1988 Jun 20;201(4):683–695. [PubMed]
  • Stern S, Powers T, Changchien LM, Noller HF. RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science. 1989 May 19;244(4906):783–790. [PubMed]
  • Valegård K, Murray JB, Stockley PG, Stonehouse NJ, Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 1994 Oct 13;371(6498):623–626. [PubMed]
  • Wittmann-Liebold B, Greuer B. The primary structure of protein S5 from the small subunit of the Escherichia coli ribosome. FEBS Lett. 1978 Nov 1;95(1):91–98. [PubMed]
  • Wolffe AP. Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. Bioessays. 1994 Apr;16(4):245–251. [PubMed]

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