4Y1I
Lactococcus lactis yybP-ykoY Mn riboswitch bound to Mn2+
Summary for 4Y1I
| Entry DOI | 10.2210/pdb4y1i/pdb |
| Related | 4Y1J 4Y1M |
| Descriptor | Lactococcus lactis yybP-ykoY riboswitch, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (6 entities in total) |
| Functional Keywords | riboswitch, manganese-binding, rna |
| Biological source | Lactococcus lactis subsp. lactis |
| Total number of polymer chains | 2 |
| Total formula weight | 69036.53 |
| Authors | Price, I.R.,Ke, A. (deposition date: 2015-02-07, release date: 2015-04-08, Last modification date: 2024-02-28) |
| Primary citation | Price, I.R.,Gaballa, A.,Ding, F.,Helmann, J.D.,Ke, A. Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches. Mol.Cell, 57:1110-1123, 2015 Cited by PubMed Abstract: Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 μM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain. PubMed: 25794619DOI: 10.1016/j.molcel.2015.02.016 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.85 Å) |
Structure validation
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