PDBsum entry 3rkf

RNA

PDB id: 3rkf

Contents

DNA/RNA

Ligands

DX4 ×4

NCO ×26

Waters ×12

PDB id:

3rkf

Name:

RNA

Title:

Crystal structure of guanine riboswitch c61u/g37a double mutant bound to thio-guanine

Structure:

Guanine riboswitch. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Synthetic: yes

Resolution:

2.50Å R-factor: 0.208 R-free: 0.226

Authors:

J.Buck,A.Wacker,E.Warkentin,J.Woehnert,J.Wirmer-Bartoschek,H.Schwalbe

Key ref:

J.Buck et al. (2011). Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res, 39, 9768-9778. PubMed id: 21890900

Date:

18-Apr-11 Release date: 17-Aug-11

DNA/RNA chains

G-G-C-C-A-U-A-U-A-A-C-U-G-C-G-U-G-G-A-U-A-U-A-G-C-A-C-G-C-A-G-G-U-U-U-C-U-A-C- 67 bases

G-G-C-C-A-U-A-U-A-A-C-U-G-C-G-U-G-G-A-U-A-U-A-G-C-A-C-G-C-A-G-G-U-U-U-C-U-A-C- 67 bases

G-G-C-C-A-U-A-U-A-A-C-U-G-C-G-U-G-G-A-U-A-U-A-G-C-A-C-G-C-A-G-G-U-U-U-C-U-A-C- 67 bases

G-G-C-C-A-U-A-U-A-A-C-U-G-C-G-U-G-G-A-U-A-U-A-G-C-A-C-G-C-A-G-G-U-U-U-C-U-A-C- 67 bases

Nucleic Acids Res 39:9768-9778 (2011)

PubMed id: 21890900

Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain.

J.Buck, A.Wacker, E.Warkentin, J.Wöhnert, J.Wirmer-Bartoschek, H.Schwalbe.

ABSTRACT

Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch from Bacillus subtilis, for example, is stabilized by extensive interactions between apical loop regions of the aptamer domain. Previously, we have shown that destabilization of this tertiary loop-loop interaction abrogates ligand binding of the G37A/C61U-mutant aptamer domain (Gsw(loop)) in the absence of Mg(2+). However, if Mg(2+) is available, ligand-binding capability is restored by a population shift of the ground-state RNA ensemble toward RNA conformations with pre-formed loop-loop interactions. Here, we characterize the striking influence of long-range tertiary structure on RNA folding kinetics and on ligand-bound complex structure, both by X-ray crystallography and time-resolved NMR. The X-ray structure of the ligand-bound complex reveals that the global architecture is almost identical to the wild-type aptamer domain. The population of ligand-binding competent conformations in the ground-state ensemble of Gsw(loop) is tunable through variation of the Mg(2+) concentration. We quantitatively describe the influence of distinct Mg(2+) concentrations on ligand-induced folding trajectories both by equilibrium and time-resolved NMR spectroscopy at single-residue resolution.