8GXB

Crystal structure of NAD+ -II riboswitch in complex with NAD+

Summary for 8GXB

• Entry DOI: 10.2210/pdb8gxb/pdb
• Descriptor: NAD+ II riboswitch, U1 small nuclear ribonucleoprotein A, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: riboswitch, nad+, noncoding rna, rna, protein-rna complex, protein/rna
• Biological source: Streptococcus sp.; More
• Total number of polymer chains: 7
• Total formula weight: 97431.70

Authors

Xu, X.C.,Ren, A.M. (deposition date: 2022-09-19, release date: 2023-01-18, Last modification date: 2024-05-29)

Primary citation

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

PubMed 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.

PubMed: 36610789
DOI: 10.1093/nar/gkac1227

Experimental method

X-RAY DIFFRACTION (2.15 Å)