4Y1J

Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+

Summary for 4Y1J

• Entry DOI: 10.2210/pdb4y1j/pdb
• Related: 4Y1I 4Y1M
• Descriptor: yybP-ykoY riboswitch, GUANOSINE-5'-TRIPHOSPHATE, STRONTIUM ION, ... (5 entities in total)
• Functional Keywords: riboswitch, manganese-binding, mutant, rna
• Biological source: Lactococcus lactis subsp. lactis
• Total number of polymer chains: 2
• Total formula weight: 70748.35

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

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: 25794619
DOI: 10.1016/j.molcel.2015.02.016

Experimental method

X-RAY DIFFRACTION (2.24 Å)