6dmc | pdb_00006dmc

ppGpp Riboswitch bound to ppGpp, native structure

spinqualitylabelsall models 6dmc, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6dmc is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: G4P, K, MG, NA NonStd Res: CCC, GTP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg(2+)-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution. ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.,Peselis A, Serganov A Nat Chem Biol. 2018 Sep;14(9):887-894. doi: 10.1038/s41589-018-0114-4. Epub 2018 , Aug 17. PMID:30120360 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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