5VJB

Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa

Summary for 5VJB

• Entry DOI: 10.2210/pdb5vjb/pdb
• Related: 5VJ9
• Descriptor: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3'), GUANIDINE, SPERMINE, ... (5 entities in total)
• Functional Keywords: guanidine, riboswitch, kissing loop, hairpin, rna
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 4
• Total formula weight: 22054.13

Authors

Reiss, C.W.,Strobel, S.A. (deposition date: 2017-04-19, release date: 2017-06-28, Last modification date: 2024-03-13)

Primary citation

Reiss, C.W.,Strobel, S.A.
Structural basis for ligand binding to the guanidine-II riboswitch.
RNA, 23:1338-1343, 2017

PubMed Abstract: The guanidine-II riboswitch, also known as , is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stem-loops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cations and functions as a translationally controlled on-switch. Here we report the structure of a P2 stem-loop from the guanidine-II riboswitch aptamer bound to guanidine at 1.57 Å resolution. The hairpins dimerize via the conserved tetraloop, which also contains the binding pocket. Two guanidinium molecules bind near the dimerization interface, one in each tetraloop. The guanidinium cation is engaged in extensive hydrogen bonding to the RNA. Contacts include the Hoogsteen face of a guanine base and three nonbridging phosphate oxygens. Cation-π interactions and ionic interactions also stabilize ligand binding. The guanidine-II riboswitch utilizes the same recognition strategies as the guanidine-I riboswitch while adopting an entirely different and much smaller RNA fold.

PubMed: 28600356
DOI: 10.1261/rna.061804.117

Experimental method

X-RAY DIFFRACTION (2.1 Å)