4RZD

Crystal Structure of a PreQ1 Riboswitch

Summary for 4RZD

• Entry DOI: 10.2210/pdb4rzd/pdb
• Descriptor: PreQ1-III Riboswitch (Class 3), 7-DEAZA-7-AMINOMETHYL-GUANINE (3 entities in total)
• Functional Keywords: three-way helical junction, hl(out)-type pseudoknot, translational regulation, rna
• Biological source: Faecalibacterium prausnitzii
• Total number of polymer chains: 1
• Total formula weight: 32818.43

Authors

Wedekind, J.E.,Liberman, J.A.,Salim, M. (deposition date: 2014-12-20, release date: 2015-07-01, Last modification date: 2024-02-28)

Primary citation

Liberman, J.A.,Suddala, K.C.,Aytenfisu, A.,Chan, D.,Belashov, I.A.,Salim, M.,Mathews, D.H.,Spitale, R.C.,Walter, N.G.,Wedekind, J.E.
Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.
Proc.Natl.Acad.Sci.USA, 112:E3485-E3494, 2015

PubMed Abstract: PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ1 binds tightly (KD,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1-P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock ∼ 0.6 s(-1)) and undocking (kundock ∼ 1.1 s(-1)). Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.

PubMed: 26106162
DOI: 10.1073/pnas.1503955112

Experimental method

X-RAY DIFFRACTION (2.75 Å)