PDBsum entry 2l1v

RNA

PDB id: 2l1v

Contents

DNA/RNA

Ligands

PRF

References listed in PDB file

Key reference

Title

Structural insights into riboswitch control of the biosynthesis of queuosine, A modified nucleotide found in the anticodon of tRNA.

Authors

M.Kang, R.Peterson, J.Feigon.

Ref.

Mol Cell, 2009, 33, 784-790. [DOI no: 10.1016/j.molcel.2009.02.019]

PubMed id

19285444

Abstract

The modified nucleotide queuosine (Q) is almost universally found in the anticodon wobble position of specific tRNAs. In many bacteria, biosynthesis of Q is modulated by a class of regulatory mRNA elements called riboswitches. The preQ(1) riboswitch, found in the 5'UTR of bacterial genes involved in synthesis of the Q precursors preQ(0) and preQ(1), contains the smallest known aptamer domain. We report the solution structure of the preQ(1) riboswitch aptamer domain from Bacillus subtilis bound to preQ(1), which is a unique compact pseudoknot with three loops and two stems that encapsulates preQ(1) at the junction between the two stems. The pseudoknot only forms in the presence of preQ(1), and the 3' A-rich tail of the aptamer domain is an integral part of the pseudoknot. In the absence of preQ(1), the A-rich tail forms part of the antiterminator. These structural studies provide insight into riboswitch transcriptional control of preQ(1) biosynthesis.

Figure 2.
Figure 2. Structure of the Complex of the Minimal preQ[1] Riboswitch Aptamer with preQ[1]
(A) Sequence and predicted hairpin-tail secondary structure of the preQ[1] riboswitch aptamer 36 queC(C14,17U), with pseudoknot elements labeled.
(B) Schematic of preQ[1] riboswitch aptamer complex fold. Hydrogen bond interactions between bases are indicated with the notation of Leontis and Westhof (Leontis and Westhof, 2001).
(C) Stereoview of stick representation of the lowest energy structure (nt 3–36, preQ[1]).
(D) van der Waals representations of the lowest-energy structure. Structural elements are colored red (P1), blue (P2), orange (L1), gold (L2), green (L3), and magenta (preQ[1]).

Figure 3.
Figure 3. The preQ[1] Binding Pocket and the A-Amino Kissing Motif
(A) Side view of the three layers of the conserved binding pocket showing the preQ[1] base quadruple, base triple above, and base quadruple below shown as sticks.
(B) Close-up view of preQ[1] in the binding pocket, shown with van der Waals surface.
(C) C33-G13-A18 (P2-L2) base triple.
(D) C19-preQ[1]-A32-U9 (L2-preQ[1]-L3-L1) base quadruple.
(E) A30-G7-C20-A31 (P1-L3) base quadruple. A30 and A31 form an A-platform and interact with the minor groove of G7-C20, respectively. The C20 2′OH appears as an unusually lowfield shifted resonance (9.01 ppm) in the proton spectra (see Figure S5).
(F) Interaction of L3 with the minor groove of P1. The bases of the A-rich L3 interact primarily with their Watson-Crick edge, forming a series of AN6H hydrogen bonds with nucleotides of P1.
(G) Interaction of A25 with G4 in P1.
(H) Interaction of A27 with A5 in P1. Color scheme is the same as in Figure 2.

The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 33, 784-790) copyright 2009.