6CC3

Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.698 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.

Bachas, S.T.Ferre-D'Amare, A.R.

(2018) Cell Chem Biol 25: 962

  • DOI: 10.1016/j.chembiol.2018.04.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn <sup>2+ </sup>. X-ray crystallography revealed a binuclear cation-binding pocket. This ...

    The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn 2+ . X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn 2+ , but how this excludes other soft cations remained enigmatic. By subjecting representative yybP-ykoY riboswitches to diverse cations in vitro, we now find that these RNAs exhibit limited transition metal ion selectivity. Among the cations tested, Cd 2+ and Mn 2+ bind most tightly, and comparison of three new Cd 2+ -bound crystal structures suggests that these riboswitches achieve selectivity by enforcing heptacoordination (favored by high-spin Cd 2+ and Mn 2+ , but otherwise uncommon) in the softer site. Remarkably, the Cd 2+ - and Mn 2+ -selective bacterial transcription factor MntR also uses heptacoordination within a binuclear site to achieve selectivity.


    Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA. Electronic address: adrian.ferre@nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (101-MER)A,B101Lactococcus lactis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.698 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.531α = 90.00
b = 68.288β = 97.96
c = 83.384γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references