Abstract
The nadA motif is the first known NAD+-dependent riboswitch, comprising two similar tandem bulged stem–loop structures. We have determined the structure of the 5′ domain 1 of the riboswitch. It has three coaxial helical segments, separated by an ACANCCCC bulge and by an internal loop, with a tertiary contact between them that includes two C:G base pairs. We have determined the structure with a number of ligands related to NADH, but in each case only the ADP moiety is observed. The adenosine adopts an anti conformation, forms multiple hydrogen bonds across the width of the sugar edge of the penultimate C:G base pair of the helix preceding the bulge, and the observed contacts have been confirmed by mutagenesis and calorimetry. Two divalent metal ions play a key structural role at the narrow neck of the bulge. One makes direct bonding contacts to the diphosphate moiety, locking it into position. Thus the nucleobase, ribose, and phosphate groups of the ADP moiety are all specifically recognized by the RNA. The NAD+ riboswitch is modular. Domain 1 is an ADP binding domain that may be ancient and could potentially be used in combination with other ligand binding motifs such as CoA.
Highlights
Riboswitches are cis-acting elements that occur predominantly in the 5′-untranslated regions of bacterial mRNA to control gene expression (Roth and Breaker 2009; Serganov and Nudler 2013; Sherwood and Henkin 2016)
Ligand binding is discussed in detail below, but we note that electron density is only visible for the ADP moiety of the NADH
It is probable that the nadA motif is an OFF riboswitch that regulates the biosynthesis of nicotinamide-adenine dinucleotide (NAD)+ in some bacteria (Malkowski et al 2019)
Summary
Riboswitches are cis-acting elements that occur predominantly in the 5′-untranslated regions of bacterial mRNA to control gene expression (Roth and Breaker 2009; Serganov and Nudler 2013; Sherwood and Henkin 2016). The gene product will be functionally related to the small molecule that binds the riboswitch, such as being an enzyme in its biosynthetic pathway. 40 classes of riboswitches have been identified to date. While the biosynthesis of many coenzymes in bacteria is controlled by riboswitches, until recently none had been identified for the coenzyme nicotinamide-adenine dinucleotide (NAD)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
