SNAP output for PDB entry 8gxb [SNAP web server]

PDB-id

8gxb; SNAP-derived features in text and JSON formats; DNAproDB

Class

protein-RNA

Method

X-ray (2.15 Å)

Summary

Crystal structure of nad+ -ii riboswitch in complex with nad+

Reference

Xu X, Egger M, Li C, Chen H, Micura R, Ren A (2023): "Structure-based investigations of the NAD+-II riboswitch." Nucleic Acids Res., 51, 54-67. doi: 10.1093/nar/gkac1227.

Abstract

Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that are essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according to phylogenetic analysis. To reveal the three-dimensional architecture and the ligand-binding mode of this riboswitch, we solved the crystal structure of NAD+-II riboswitch in complex with NAD+. Strikingly and in contrast to class-I riboswitches that form a tight recognition pocket for the adenosine diphosphate (ADP) moiety of NAD+, the class-II riboswitches form a binding pocket for the nicotinamide mononucleotide (NMN) portion of NAD+ and display only unspecific interactions with the adenosine. We support this finding by an additional structure of the class-II RNA in complex with NMN alone. The structures define a novel RNA tertiary fold that was further confirmed by mutational analysis in combination with isothermal titration calorimetry (ITC), and 2-aminopurine-based fluorescence spectroscopic folding studies. Furthermore, we truncated the pnuC RNA motif to a short RNA helical scaffold with binding affinity comparable to the wild-type motif to allude to the potential of engineering the NAD+-II motif for biotechnological applications.