PDBsum entry 3dir

RNA

PDB id: 3dir

Contents

DNA/RNA

Ligands

IEL

Metals

__K

_NA ×11

Waters ×11

PDB id:

3dir

Name:

RNA

Title:

Crystallization of the thermotoga maritima lysine riboswitch bound to n6-1-iminoethyl-l-lysine

Structure:

RNA (174-mer). Chain: a. Engineered: yes

Source:

Synthetic: yes. Other_details: in vitro transcribed RNA from the thermotoga maritima msb8 asd gene

Resolution:

2.90Å R-factor: 0.180 R-free: 0.211

Authors:

A.A.Serganov

Key ref:

A.Serganov et al. (2008). Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature, 455, 1263-1267. PubMed id: 18784651 DOI: 10.1038/nature07326

Date:

20-Jun-08 Release date: 16-Sep-08

DNA/RNA chain

GTP-G-C-C-G-A-C-G-G-A-G-G-C-G-C-G-C-C-C-G-A-G-A-U-G-A-G-U-A-G-G-C-U-G-U-C-C-C- 174 bases

DOI no: 10.1038/nature07326

Nature 455:1263-1267 (2008)

PubMed id: 18784651

Structural insights into amino acid binding and gene control by a lysine riboswitch.

A.Serganov, L.Huang, D.J.Patel.

ABSTRACT

In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 ångström (A)) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K(+)-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

Selected figure(s)

Figure 1.
Figure 1: Overall structure and long-range tertiary interactions of the lysine-bound T. maritima riboswitch. a, Schematic of the riboswitch fold observed in the crystal structure of the complex. The bound lysine is in red. The RNA domains are depicted in colours used for subsequent figures. Base-specific tertiary contacts and long-range stacking interactions are shown as thin green and thick blue dashed lines, respectively. Nucleotides invariant in known lysine riboswitches are boxed. b, c, Overall lysine riboswitch structure in a ribbon representation showing front (b) and rotated by 60° (c) views. d, The L2–L3 kissing loop interaction is formed by six base pairs, supplemented by interstrand stacking interactions between A42 and C95, G43 and U94, and G44 and G101. Hydrogen bonds between interstrand base pairs and orthogonally aligned G43 and U94 bases are depicted by dashed lines. e, The L4-loop–P2-helix interaction formed by an insertion of the A126–A127–A129 stack of L4 into the RNA groove of P2 distorted by non-canonical base pairs.

Figure 2.
Figure 2: Structure and interactions in the junctional region of the lysine riboswitch. a, Stereo view of the junction with bound lysine. Green sphere depicts a K^+ cation. b, Details of riboswitch lysine interactions. Lysine is positioned within the omit F[o] - F[c] electron density map contoured at 3.5 level. Water molecules are shown as light blue spheres. K^+ cation coordination and hydrogen bonds are depicted by dashed lines. c, Direct and water-mediated interactions involving -ammonium group of lysine. d, e, Interactions in the top (d) and middle (e) junctional layers.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 455, 1263-1267) copyright 2008.

Figures were selected by an automated process.