5NEX

The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with agmatine

Summary for 5NEX

• Entry DOI: 10.2210/pdb5nex/pdb
• Descriptor: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3'), SODIUM ION, AGMATINE, ... (4 entities in total)
• Functional Keywords: guanidine ii riboswitch, stem-loop, tetra loop, dimer, rna, agmatine
• Biological source: Gloeobacter violaceus
• Total number of polymer chains: 1
• Total formula weight: 6194.55

Authors

Huang, L.,Wang, J.,Lilley, D.M.J. (deposition date: 2017-03-13, release date: 2017-05-31, Last modification date: 2024-05-08)

Primary citation

Huang, L.,Wang, J.,Lilley, D.M.J.
The Structure of the Guanidine-II Riboswitch.
Cell Chem Biol, 24:695-702.e2, 2017

PubMed Abstract: The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.

PubMed: 28529131
DOI: 10.1016/j.chembiol.2017.05.014

Experimental method

X-RAY DIFFRACTION (1.72 Å)