5DDQ: L-glutamine Riboswitch Bound With L-glutamine Soaked With Mn2+

Citation:
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.
PDB ID: 5DDQDownload
MMDB ID: 135057
PDB Deposition Date: 2015/8/25
Updated in MMDB: 2015/12
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Synechococcus elongatus
Similar Structures:
Biological Unit for 5DDQ: dimeric; determined by author and by software (PISA)
Molecular Components in 5DDQ
Label Count Molecule
Protein (1 molecule)
1
U1 Small Nuclear Ribonucleoprotein a(Gene symbol: SNRPA)
Molecule annotation
Nucleotide(1 molecule)
1
L-glutamine Riboswitch RNA (61-mer)
Molecule annotation
Chemicals (11 molecules)
1
1
2
2
3
1
4
7
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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