5DDR

L-glutamine riboswitch bound with L-glutamine soaked with Cs+

Summary for 5DDR

• Entry DOI: 10.2210/pdb5ddr/pdb
• Related: 5DDO 5DDP 5DDQ
• Descriptor: L-glutamine riboswitch RNA (61-MER), U1 small nuclear ribonucleoprotein A, GLUTAMINE, ... (8 entities in total)
• Functional Keywords: riboswitch, l-glutamine, bound-form, rna, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 63755.51

Authors

Ren, A.,Patel, D.J. (deposition date: 2015-08-25, release date: 2015-12-23, Last modification date: 2024-03-06)

Primary citation

Ren, A.,Xue, Y.,Peselis, A.,Serganov, A.,Al-Hashimi, H.M.,Patel, D.J.
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.
Cell Rep, 13:1800-1813, 2015

PubMed Abstract: Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational transition in the Synechococcus elongatus glutamine riboswitch from tuning fork to L-shaped alignment of stem segments. This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg(2+)-mediated intermolecular interactions. The transition also stabilizes the P1 helix through a long-range "linchpin" Watson-Crick G-C pair-capping interaction, while melting a short helix below P1 potentially capable of modulating downstream readout. NMR data establish that the ligand-free glutamine riboswitch in Mg(2+) solution exists in a slow equilibrium between flexible tuning fork and a minor conformation, similar, but not identical, to the L-shaped bound conformation. We propose that an open ligand-binding pocket combined with a high conformational penalty for forming the ligand-bound state provide mechanisms for reducing binding affinity while retaining high selectivity.

PubMed: 26655897
DOI: 10.1016/j.celrep.2015.10.062

Experimental method

X-RAY DIFFRACTION (2.605 Å)