4Y1M

An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state

  • Classification: RNA
  • Organism(s): Escherichia coli

  • Deposited: 2015-02-08 Released: 2015-04-08 
  • Deposition Author(s): Price, I.R., Ke, A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.

Price, I.R.Gaballa, A.Ding, F.Helmann, J.D.Ke, A.

(2015) Mol.Cell 57: 1110-1123

  • DOI: 10.1016/j.molcel.2015.02.016
  • Primary Citation of Related Structures:  

  • 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+)-d ...

    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.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
E. coli yybP-ykoY riboswitchB,A107Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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Download CCD File 
A, B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 159.384α = 90.00
b = 159.384β = 90.00
c = 277.108γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
SHELXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-08 
  • Released Date: 2015-04-08 
  • Deposition Author(s): Price, I.R., Ke, A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM086766
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM 102543

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Data collection
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations