PDBsum entry 3f4h

RNA

PDB id: 3f4h

Contents

DNA/RNA

Ligands

RS3

Metals

_MG ×11

__K ×2

Waters ×1

References listed in PDB file

Key reference

Title

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.

Authors

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

Ref.

Nature, 2009, 458, 233-237. [DOI no: 10.1038/nature07642]

PubMed id

19169240

Abstract

The biosynthesis of several protein cofactors is subject to feedback regulation by riboswitches. Flavin mononucleotide (FMN)-specific riboswitches, also known as RFN elements, direct expression of bacterial genes involved in the biosynthesis and transport of riboflavin (vitamin B(2)) and related compounds. Here we present the crystal structures of the Fusobacterium nucleatum riboswitch bound to FMN, riboflavin and antibiotic roseoflavin. The FMN riboswitch structure, centred on an FMN-bound six-stem junction, does not fold by collinear stacking of adjacent helices, typical for folding of large RNAs. Rather, it adopts a butterfly-like scaffold, stapled together by opposingly directed but nearly identically folded peripheral domains. FMN is positioned asymmetrically within the junctional site and is specifically bound to RNA through interactions with the isoalloxazine ring chromophore and direct and Mg(2+)-mediated contacts with the phosphate moiety. Our structural data, complemented by binding and footprinting experiments, imply a largely pre-folded tertiary RNA architecture and FMN recognition mediated by conformational transitions within the junctional binding pocket. The inherent plasticity of the FMN-binding pocket and the availability of large openings make the riboswitch an attractive target for structure-based design of FMN-like antimicrobial compounds. Our studies also explain the effects of spontaneous and antibiotic-induced deregulatory mutations and provided molecular insights into FMN-based control of gene expression in normal and riboflavin-overproducing bacterial strains.

Figure 1.
Figure 1: Overall structure and tertiary interactions of the FMN-bound F. nucleatum riboswitch. a, Homology-based schematic of the FMN riboswitch with key long-range interactions indicated by arrows. RNA segments are depicted in colours used for subsequent figures. b, Schematic of the riboswitch fold observed in the crystal structure of the complex. The bound FMN is in red. Key stacking interactions involving FMN are shown as blue dashed lines. Nucleotides that are more than 95% conserved among 183 FMN riboswitches are boxed. c, Overall riboswitch structure in a ribbon representation. d, Superposition of the P2–P6 (nucleotides 10–32 and 85–98) and P3–P5 domains (nucleotides 62–84 and 33–46). The root mean square deviation is 1.8 Å. e, f, Distinct alignments of nucleotide triples in the P2–P6 (e) and P3–P5 (f) domains. Dashed lines depict putative hydrogen bonds. Distances are in ångstroms.

Figure 3.
Figure 3: Interactions of FMN analogues with the riboswitch. a, All-atom superposition of the ligand-binding pocket for riboflavin-bound (blue and green) and FMN-bound (grey) riboswitches. Nucleotides in green are positioned within hydrogen-bond distances of the ribityl moiety of riboflavin. b, Superposition of riboflavin-bound (blue) and roseoflavin-bound (pink and green) riboswitches, depicted as in a. c, Surface view inside of the FMN-bound riboswitch with large openings shown with red arrows.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2009, 458, 233-237) copyright 2009.