Edwards et al., Curr Opin Struct Biol 2007

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274 Nucleic acids Figure 1 Crystal structures of riboswitch–effector complexes, and schematic depiction of conserved primary and secondary structures. (a,b) Purine riboswitch (PDB code 1U8D), (c,d) TPP riboswitch (PDB code 2GDI), (e,f) SAM riboswitch (PDB code 2GIS) and (g,h) glmS ribozyme-riboswitch (PDB code 2H0Z). The 3 0 half of the P1 helices, which participate in the genetic switch event, is colored red, and tertiary interactions thought to be important in folding and RNA–metabolite complex stability are green. Bound metabolites are shown in blue; PK and KT denote pseudoknots and K-turns, respectively; ‘var’ indicates an RNA segment of phylogenetically variable length and composition. Filled spheres indicate that the sequence is not conserved, but the Watson–Crick pairing is. Current Opinion in Structural Biology 2007, 17:273–279 www.sciencedirect.com
Metabolite recognition by riboswitches Edwards, Klein and Ferré-D’Amaré 275 structure of the metabolite-binding domain of the first class to be discovered (the SAM-I riboswitch) reveals an architecture that is distinctly different from the inverted-h fold of the purine and TPP riboswitches (Figure 1e,f) [15 ]. The SAM-I riboswitch contains two stacks (P1-P4 and P2a-P3) that, rather than packing sideby-side, cross at an angle of 708. A pseudoknot coupled to a kink-turn [16] atop P2 appears to stabilize this fold. The SAM-binding site is located at the interface of the minor grooves of P1 and P3, and has features reminiscent of the metabolite-binding sites of both the TPP and the purine riboswitches. Like TPP, SAM bridges two helical stacks. Like the purine riboswitches, SAM makes van der Waals contact with the 3 0 strand of the P1 switch helix. In many Gram-positive bacteria, the glmS ribozyme-riboswitch is part of the 5 0 -UTR of the mRNA that encodes glucosamine-6-phosphate (GlcN6P) synthetase [17]. This riboswitch has a self-cleavage activity that becomes activated when it binds GlcN6P. The structure of the glmS ribozyme [18 ,19 ] consists of three parallel helical stacks (Figure 1g,h). A doubly pseudoknotted core (P1-P2-P2.1- P2.2) is buttressed by a peripheral RNA domain (P4-P4.1). The solvent-exposed GlcN6P-binding pocket is composed of two highly distorted major grooves and abuts the site of self-cleavage, reflecting the coenzyme function of GlcN6P (see the review by Scott in this issue). Among currently characterized riboswitches, the glmS ribozyme is unique because it adopts its active structure in the absence of its metabolite ligand [18 ,20 ]. As other ribozymes, such as the natural hairpin ribozyme [21,22] and the in vitro selected Diels–Alderase [23], also assemble rigid active sites, this disparity might reflect the different constraints under which ribozymes and RNAs that function by alternative folding evolved. Ligand recognition by riboswitches The purine riboswitch recognizes its ligand almost exclusively through hydrogen-bonding interactions that satisfy nearly all possible acceptors and donors of the purine (Figure 2a). Purine riboswitch structures have been solved bound to 2,6-diaminopurine [24 ] and 2,4,6-triaminopyrimidine [25], in addition to the biological activators hypoxanthine [6], guanine [7] and adenine [7]. The purine ligand is primarily recognized by residue 74 of the riboswitch, a pyrimidine, through Watson–Crick pairing [6,7,26]. In addition, U51 and the 2 0 -OH of U22 hydrogen bond to the N3/N9 edge (corresponding to the sugar edge of nucleotides) and the N7, respectively, of the purine. Reliance on Watson–Crick (as opposed to Hoogsteen) pairing for recognition enables the same RNA scaffold to regulate either adenine or guanine metabolism by having U74 or C74, respectively. Gilbert et al.[24 ] noted that the purine ligand makes poor stacking interactions and proposed that this enhances the discriminatory role of Watson–Crick pairing with residue 74. The two helical stacks of the thi-box riboswitch separately recognize the aminopyrimidine and pyrophosphate moieties of TPP. J3/2 of the ‘pyrimidine sensor helix’ (the P1- P2-P3 stack) adopts a canonical T-loop fold [9 ,10 ,11 ]. Binding of the aminopyrimidine ring of TPP to G40 of this T-loop (Figure 2b) mimics a tertiary interaction between the D- and T-loops in the classic L-shaped fold of tRNA. The aminopyrimidine of TPP and G40 replace G18 and C55, respectively (purines and pyrimidines are reversed between the riboswitch and the tRNA). Mimicry of an all- RNA structure by an exogenous small molecule is reminiscent of ATP binding by an in vitro selected aptamer RNA, whereby the ATP completes a GNRA tetraloop [27,28]. Rather than directly binding to the negatively charged pyrophosphate of TPP, the ‘pyrophosphate sensor helix’ (the P4-P5 stack) of the riboswitch coordinates the pyrophosphate mostly through two solvated divalent metals ions (the exception is G78) [9 ,10 ,11 ,29]. Thus, the riboswitch effectively binds a positively charged TPP– cation complex. Structures of the TPP riboswitch bound to three metabolite analogs suggest that the pyrimidine sensor helix is largely preformed, whereas the pyrophosphate sensor helix becomes organized concomitant with binding of the TPP–cation complex [11 ]. The SAM-I riboswitch sandwiches its ligand between two parallel helices [15 ]. P1 recognizes the ribose–sulfur backbone of SAM primarily through van der Waals contacts (Figure 2c). By contrast, the P3 helix binds the adenine ring and the amino acid by making several hydrogen bonds and stacking interactions. Interestingly, the RNA does not directly recognize the methionine e-methyl group. Rather, the positively charged sulfur atom makes a favorable electrostatic interaction with the partial negative charge on O2 of U7. This might explain the enhanced binding of SAM compared to S-adenosylhomocysteine and other non-positively charged analogs [12,30]. Recognition of GlcN6P, a simple phosphorylated hexosamine sugar, by the glmS ribozyme-riboswitch presents a challenge for RNA that is distinct from those posed by purines, TPP and SAM, all of which have nucleotide-like substructures. Crystal structures of the glmS ribozymeriboswitch were solved bound to glucose-6-phosphate (Glc6P), an isosteric competitive inhibitor (antagonist) of GlcN6P [18 ], and to the authentic activator GlcN6P ([19 ]; DJ Klein and AR Ferré-D’Amaré, unpublished), revealing that GlcN6P and Glc6P are equivalently positioned in the glmS ribozyme-riboswitch active site. The sugar hydroxyl groups hydrogen bond to G1, C2, A50 and G65 (Figure 2d). The amine of GlcN6P hydrogen bonds to a water molecule, U51 and the 5 0 oxygen of G1; the last is the leaving group of the transesterification reaction catalyzed by the ribozyme. As in the TPP riboswitch, the phosphate of the metabolite interacts with the RNA through two solvated divalent metal ions ([19 ]; DJ Klein and AR Ferré-D’Amaré, unpublished). TPP, SAM and www.sciencedirect.com Current Opinion in Structural Biology 2007, 17:273–279
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Edwards et al., Curr Opin Struct Biol 2007

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