8FZA

Class I type III preQ1 riboswitch from E. coli

Summary for 8FZA

• Entry DOI: 10.2210/pdb8fza/pdb
• Related: 6vuh 6vui 7rex 8fb3
• Descriptor: PreQ1 Riboswitch (30-MER), 7-DEAZA-7-AMINOMETHYL-GUANINE, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: riboswitch, prequeuosine1, preq1, pseudoknot, a-amino kissing, bound state, rna
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 19645.55

Authors

Wedekind, J.E.,Schroeder, G.M.,Jenkins, J.L. (deposition date: 2023-01-27, release date: 2023-08-30, Last modification date: 2023-10-18)

Primary citation

Schroeder, G.M.,Kiliushik, D.,Jenkins, J.L.,Wedekind, J.E.
Structure and function analysis of a type III preQ 1 -I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence.
J.Biol.Chem., 299:105208-105208, 2023

PubMed Abstract: Riboswitches are small noncoding RNAs found primarily in the 5' leader regions of bacterial messenger RNAs where they regulate expression of downstream genes in response to binding one or more cellular metabolites. Such noncoding RNAs are often regulated at the translation level, which is thought to be mediated by the accessibility of the Shine-Dalgarno sequence (SDS) ribosome-binding site. Three classes (I-III) of prequeuosine (preQ)-sensing riboswitches are known that control translation. Class I is divided into three subtypes (types I-III) that have diverse mechanisms of sensing preQ, which is involved in queuosine biosynthesis. To provide insight into translation control, we determined a 2.30 Å-resolution cocrystal structure of a class I type III preQ-sensing riboswitch identified in Escherichia coli (Eco) by bioinformatic searches. The Eco riboswitch structure differs from previous preQ riboswitch structures because it has the smallest naturally occurring aptamer and the SDS directly contacts the preQ metabolite. We validated structural observations using surface plasmon resonance and in vivo gene-expression assays, which showed strong switching in live E. coli. Our results demonstrate that the Eco riboswitch is relatively sensitive to mutations that disrupt noncanonical interactions that form the pseudoknot. In contrast to type II preQ riboswitches, a kinetic analysis showed that the type III Eco riboswitch strongly prefers preQ over the chemically similar metabolic precursor preQ. Our results reveal the importance of noncanonical interactions in riboswitch-driven gene regulation and the versatility of the class I preQ riboswitch pseudoknot as a metabolite-sensing platform that supports SDS sequestration.

PubMed: 37660906
DOI: 10.1016/j.jbc.2023.105208

Experimental method

X-RAY DIFFRACTION (2.3 Å)