Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 A. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C-G base pairs on one side and sheared G-A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5'-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.

The glmS ribozyme is the only natural catalytic RNA known to require a small-molecule activator for catalysis. This catalytic RNA functions as a riboswitch, with activator-dependent RNA cleavage regulating glmS messenger RNA expression. We report crystal structures of the glmS ribozyme in precleavage states that are unliganded or bound to the competitive inhibitor glucose-6-phosphate and in the postcleavage state. All structures superimpose closely, revealing a remarkably rigid RNA that contains a preformed active and coenzyme-binding site. Unlike other riboswitches, the glmS ribozyme binds its activator in an open, solvent-accessible pocket. Our structures suggest that the amine group of the glmS ribozyme-bound coenzyme performs general acid-base and electrostatic catalysis.

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Both monovalent cations and magnesium ions are well known to be essential for the folding and stability of large RNA molecules that form complex and compact structures. In the atomic structure of the large ribosomal subunit from Haloarcula marismortui, we have identified 116 magnesium ions and 88 monovalent cations bound principally to rRNA. Although the rRNA structures to which these metal ions bind are highly idiosyncratic, a few common principles have emerged from the identities of the specific functional groups that coordinate them. The nonbridging oxygen of a phosphate group is the most common inner shell ligand of Mg

Riboswitches are mRNA domains that bind metabolites and modulate gene expression in cis. We report cocrystal structures of a remarkably compact riboswitch (34 nucleotides suffice for ligand recognition) from Bacillus subtilis selective for the essential nucleobase preQ 1 (7-aminomethyl-7-deazaguanine). These reveal a previously unrecognized pseudoknot fold, and suggest a conserved gene-regulatory mechanism whereby ligand binding promotes sequestration of an RNA segment that otherwise assembles into a transcriptional anti-terminator.Queuosine (Q) is a post-transcriptional modification of the wobble position of GUN anticodons of certain bacterial and eukaryal tRNAs. It is important for translational fidelity (reviewed in ref. 1). During tRNA maturation, a transglycosylase replaces the guanine at this pre-tRNA position with free preQ 1 , which is subsequently elaborated into Q. The 5'-untranslated region (UTR) of an operon encoding Q biosynthetic enzymes in many bacteria harbors a preQ 1 -specific riboswitch, consistent with regulation of the pathway by the last small-molecule intermediate in the biogenesis of Q (ref. 2). Sequence differences define two sub-types of class-I preQ 1 riboswitches, which probably employ the same metabolite recognition motif 2 . Structurally distinct (class-II) preQ 1 -responsive riboswitches were recently described 3 .Sequence analyses led Roth et al., to propose that class-I preQ 1 riboswitches consist simply of a stem-loop followed by a short single-stranded segment 2 . Characterization of the B. subtilis queC 5'-UTR demonstrated that an RNA as short as 34 nucleotides (nt) binds preQ 1 (K d ~20 nM), discriminating between preQ 1 and G through the 7-aminomethyl group unique to the former 2 . To elucidate how such a small RNA achieves high affinity binding of an essential metabolite, and to provide a framework to understand how this riboswitch modulates gene expression, we determined preQ 1 complex structures of the 34-nt core of the class I, sub-type II B. subtilis preQ 1 riboswitch 2 and of a sequence variant 4 , at 2.85 and 2.2 Å resolution, respectively (Supplementary Figs. 1 (Figs. 1a,b). Two stems separated by three loops define this most abundant type of pseudoknot. In H-type pseudoknots, loops L1 and L3 lie in the major and minor grooves of stems S2 and S1, respectively. L1 and L3 are typically uracil and adenine rich, respectively (reviewed in ref.7). The preQ 1 riboswitch conforms to these trends with an L1 of two uracils, and an L3 of seven adenines and one uracil. U6 and U7 of L1 make Watson-Crick•Hoogsteen pairs with A29 and A30, the last two nucleotides of L3. L3 residues often form triplex interactions 7 . L3 of the preQ 1 riboswitch is noteworthy for the sheer density of these, including inclined adenosine Hoogsteen face interactions (different from the glmS and SAM-II riboswitch "inclined A-minor" motif8,9), interactions with L1, and with preQ 1 (Fig. 1c, and Supplementary Table 2 online). As in other H-type pseudoknots 10 , divalent cations stabilize the sharp...