title: Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.
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.
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Aiming
authors.initials: A
authors.lastname: Ren
authors.affiliation: Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Alla
authors.initials: A
authors.lastname: Peselis
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Serganov
authors.affiliation: Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: hashim.al.hashimi@duke.edu.
authors.forename: Hashim M
authors.initials: HM
authors.lastname: Al-Hashimi
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.
authors.forename: Dinshaw J
authors.initials: DJ
authors.lastname: Patel
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D005973:Glutamine / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D058928:Riboswitch / Q000502:physiology*; D046940:Synechococcus / Q000235:genetics / Q000378:metabolism
chemical_list: D008024:Ligands; D058928:Riboswitch; D005973:Glutamine; D008274:Magnesium