6N2V

Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)

  • Classification: RNA
  • Organism(s): Xanthomonas oryzae

  • Deposited: 2018-11-14 Released: 2019-10-02 
  • 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: 2.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Local-to-global signal transduction at the core of a Mn2+sensing riboswitch.

Suddala, K.C.Price, I.R.Dandpat, S.S.Janecek, M.Kuhrova, P.Sponer, J.Banas, P.Ke, A.Walter, N.G.

(2019) Nat Commun 10: 4304-4304

  • DOI: 10.1038/s41467-019-12230-5

  • PubMed Abstract: 
  • The widespread Mn <sup>2+ </sup>-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn <sup>2+ </sup> homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas o ...

    The widespread Mn 2+ -sensing yybP-ykoY riboswitch controls the expression of bacterial Mn 2+ homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg 2+ . Only upon adding sub-millimolar Mn 2+ , however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn 2+ in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA. ailong.ke@cornell.edu.,Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno, 612 65, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic.,Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA. nwalter@umich.edu.,Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
X. oryzae Mn riboswitch optimized constructA,B99Xanthomonas oryzae
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-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

Download SDF File 
Download CCD File 
A, B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A, B
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.296α = 90.00
b = 85.167β = 90.00
c = 92.463γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-11-14 
  • Released Date: 2019-10-02 
  • Deposition Author(s): Price, I.R., Ke, A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM116632
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118174

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release