RNA protein complexes

Current Opinion in Structural Biology

Volumn 9, Issue 1, 1999, Pages 66-73

  Cusack, Stephen ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; BACTERIAL ENZYME; RNA BINDING PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; TRANSFER RNA;

AMINO TERMINAL SEQUENCE; ANTICODON; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; REVIEW;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0032864042     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80009-8     Document Type: Article

References (34)

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4. Allison TJ, Wood TC, Briercheck DM, Rastinejad F, Richardson JP, Rule GS Crystal structure of the RNA-binding domain from transcription termination factor rho. Nat Struct Biol. 5:1998;352-356. The rho protein is a hexamer of identical 47 kDa subunits that aids the release of nascent transcripts from the transcription complex. The monomer has an N-terminal RNA-binding domain and a C-terminal ATPase domain. The crystal structure of the RNA-binding domain (residues 1-130) of E. coli rho has been determined at 1.55 Å resolution. It was found to comprise three N-terminal helices sitting on top of a classical OB fold β-barrel domain. The OB fold is found in a number of other proteins that bind single-stranded RNA, such as the bacterial cold-shock protein, the anticodon-binding domain of class IIb aminoacyl-tRNA synthetases and ribosomal proteins S1 and S17.
5. •] have been determined for the 73 N-terminal residues of the influenza nonstructural protein 1 (NS1). This multifunctional RNA-binding protein suppresses normal cellular functions during influenza virus infection by inhibiting the splicing of pre-mRNA, inhibiting nuclear export of polyadenylated mRNAs and blocking inactivation of translation by PKR kinase. The RNA-binding activity resides in the N-terminal domain of the protein, which forms an all-helical dimer with three helices per subunit. The fold of the monomer has some similarity with the engrailed homeodomain protein. The RNA targets of NS1 are apparently various (polyadenine, U6 snRNA and double-stranded RNA) and they may bind to different surfaces of the protein, which has several regions of overall positive charge due to the concentration of basic residues.
6. •].
7. Keenan RJ, Freymann DM, Walter P, Stroud RM Crystal structure of the signal sequence binding subunit of the signal recognition particle. Cell. 94:1998;181-191. The signal recognition particle (SRP) protein Ffh is a universally conserved three-domain protein comprising a N-terminal helical domain, a central GTPase domain and a C-terminal methionine-rich (M) domain. The M domain is responsible for the binding of Ffh to a conserved helix of SRP RNA and is also the principle binding site for the hydrophobic signal peptide that SRP recognises on the ribosome-bound nascent chain. The crystal structure of full-length Thermus aquaticus Ffh at 3.2 Å resolution shows that the 100 residue M domain is loosely linked to the other domains and contains four amphipathic helices. The arginine-rich region, shown by mutational analysis to be critical for SRP RNA binding, is located on an outward facing helix-turn-helix motif that is similar to those found in a class of DNA-binding proteins. A hydrophobic groove between a long loop and three helices is the putative signal-peptide-binding site.
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12. •]. Circular permutation of this RNA shows that the binding domain corresponds to an independently folding RNA domain, since the 5′ and 3′ ends are not required provided that they are linked flexibly.
13. Birse D, Kapp U, Strub K, Cusack S, Åberg A The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14. EMBO J. 16:1997;3757-3766. The SRP14/9 heterodimer binds to the Alu domain of the mammalian signal recognition particle (SRP) RNA, which is responsible for the elongation arrest activity of SRP. The crystal structure at 2.5 Å resolution shows that SRP9 and SRP14 are structurally homologous, both containing the same αβββα fold that is related to but is distinct from the dsRNA-binding module. The heterodimer has pseudo-twofold symmetry and is saddle-like, comprising a strongly curved six-stranded amphipathic β sheet, with four helices packed on the convex side and the exposed concave surface being lined with positively charged residues and one aromatic residue.
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15. Correll CC, Freeborn B, Moore PB, Steitz TA Use of chemically modified nucleotides to determine a 62-nucleotide RNA crystal structure: a survey of phosphorothioates, Br, Pt and Hg. J Biomol Struct Dyn. 15:1997;165-172.
16. Oubridge C, Ito N, Evans PR, Teo CH, Nagai K Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372:1994;432-438.
17. Price SR, Evans PR, Nagai K Crystal structure of the spliceosomal U2B′-U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature. 394:1998;645-650. The U2B″ protein is 75% homologous to the U1A protein and contains an RNP module. The U2A′ protein contans leucine-rich repeats. The U2B″-U2A′ complex specifically binds a stem-loop from U2 snRNA that is similar to the U1 snRNA stem-loop that binds to U1A. The crytal structure of the U2B″-U2A′-RNA complex reveals how the RNA-binding specificity of the RNP module of U2B″ is modulated by the presence of U2A′
18. ••].
19. Ryter JM, Schultz SC Molecular basis of double-stranded RNA protein interactions: structure of a dsRNA binding domain complexed with dsRNA. EMBO J. 17:1998;6819-6826. The dsRNA-binding module (approximately 65 residues) is found in diverse proteins that bind nonspecifically to dsRNA. The structure of this module complexed with a 10 base pair RNA duplex has been determined at 1.9 Å resolution and reveals that three distinct regions of the protein interact with the RNA, mainly with the phosphodiester backbone and 2′ hydroxyl groups of the riboses.
20. •A72 mismatch pair, which is broken upon complex formation.
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25. Pro isoacceptors.
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27. lys transcript: anti-codon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 15:1996;6321-6334.
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29. Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA A 9 Å resolution X-ray crystallographic map of the large ribosomal subunit. Cell. 93:1998;1105-1115. A 9 Å map of the 50S ribosomal subunit from Haloarcula marismortui was calculated from phases given by three separate derivatives containing 18 tungsten, 11 tungsten and tantalum clusters. The metal cluster sites were located with the help of an electron microscopy model, which was positioned and orientated in the unit cell by molecular replacement. The map shows long continuous rods of density that can be attributed to ribosomal RNA.
30. Stams T, Niranjanakumari S, Fierke CA, Christianson DW Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science. 280:1998;752-755. RNase P catalyses the maturation of the 5′ end of tRNAs. The bacterial enzyme comprises an approximately 400 nucleotide RNA and an approximately 120 residue protein subunit. The RNA alone is sufficient to catalyse the reaction in vitro but the protein subunit is essential for physiological activity. The crystal structure of the Bacillus subtilus RNase P protein at 2.6 Å resolution shows that the protein has an α(A)βββα(B)βα(X) topology, with three potential RNA-binding regions: a conserved basic region that occurs on an unusual left-handed βα(B)β crossover connection; a central cleft formed by the β-sheet surface and helix A that has three exposed aromatic residues that could stack with RNA bases; and a carboxylate-rich putative metal-binding loop. The protein core topology is similar to that found in ribosomal protein S5 and domain IV of EF-G, each of which contains a left-handed βαβ crossover that is presumed to be involved in RNA binding.
31. Li H, Trotta CR, Abelson J Crystal structure and evolution of a transfer RNA splicing enzyme. Science. 280:1998;279-284. The crystal structure of the homotetrameric tRNA splicing endonuclease of Methanococcus jannaschii has been determined at 2.3 Å resolution. This enzyme excises a pseudosymmetric intron, comprising two bulged loops of three bases separated by a helical stem of four base pairs, found in the anticodon stem of pre-tRNAs. The enzyme monomer has two distinct α/β domains. The homotetramer has unusual internal symmetry and is most accurately described as a dimer of dimers, an arrangement that can explain the more complex subunit structures found in other Archaea and eukaryotic organisms. Only two of the active sites are likely to be involved in cleavage, which probably occurs by a mechanism similar to that of RNase A and involving a His-Tyr-Lys triad.
32. Tomchick DR, Turner RJ, Switzer RL, Smith JL Adaptation of an enzyme to regulatory function: structure of Bacillus subtilus PyrR a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure. 6:1998;337-350. The PyrR protein binds to specific 28-30 nucleotide stem-loop structures in mRNAs for certain pyrimidine nucleotide biosynthetic proteins. This disrupts an alternative antiterminator stem-loop, allowing the formation of a downstream terminator structure and hence attenuating transcription. This is a response to excess UMP, which is a co-regulator, binding to PyrR and increasing its RNA-binding affinity. The 1.6 Å resolution structure of PyrR shows that it is structurally similar to other phosphoribosyltransferases (PRTases), but with a novel dimer interface that creates an extensive and basic concave putative RNA-binding surface. As PyrR retains some low level, but probably biologically insignificant, uracil PRTase activity, it seems to be a good example of evolution from an enzyme of a protein regulating gene expression.
33. van Tilbeurgh H, Manival X, Aymerich S, Lhoste J-M, Dumas C, Kochoyan M Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilus. EMBO J. 16:1997;5030-5036. In the presence of the inducer sucrose, SacY binds to an antiterminator stem-loop in the mRNA of the sacB gene product (a sucrose metabolising enzyme) and prevents early transcriptional termination. The 2.0 Å resolution crystal structure of the N-terminal 55 residues of SacY that form the RNA-binding domain shows that it is dimeric, with each monomer comprising a simple four-stranded β sheet. The mode of RNA binding is currently unknown, but is likely to be different from other more well-known RNA-binding motifs.
34. Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SEV, Stockley PG Crystal structures of an RNA aptamer-protein complex at 2.8 Å resolution. Nat Struct Biol. 5:1998;133-139. The crystal structure of the wildtype RNA stem-loop operator (a 19-mer) with bound RNA bacteriophage MS2 coat protein has been previously dtermined in the context of the T = 3 icosahedral protein capsid. This article describes the ongoing use of this system as a vehicle for studying protein-RNA interactions by presenting the structure of the capsid containing an RNA stem-loop aptamer, denoted F6. This variant differs from the wildtype operator in having a three base loop (instead of a tetraloop) and an additional base pair between this loop and an important recognition element in the stem, an unpaired adenosine (A10). Remarkably, it is found that the principal sequence-specific protein-RNA interactions are very similar to the wildtype and this is achieved by the aptamer adopting a conformation in which the structure of the 5′ strand (including the bulged out base A10) is closely supperposable on that of the wildtype, whereas the 3′ strand (which does not interact with the protein) shows a concerted shift in position.