5T83

Structure of a guanidine-I riboswitch from S. acidophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.

Reiss, C.W.Xiong, Y.Strobel, S.A.

(2017) Structure 25: 195-202

  • DOI: 10.1016/j.str.2016.11.020

  • PubMed Abstract: 
  • The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specif ...

    The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 Å resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-π interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.


    Related Citations: 
    • Metabolism of Free Guanidine in Bacteria is Regulated by Widespread Riboswitch Classes
      Nelson, J.W.,Atilho, R.M.,Sherlock, M.E.,Reiss, C.W.,Strobel, S.A.,Stockbridge, R.B.,Breaker, R.R.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (95-MER)A95Sulfobacillus acidophilus DSM 10332
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

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Download CCD File 
A
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
SPK
Query on SPK

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Download CCD File 
A
SPERMINE (FULLY PROTONATED FORM)
C10 H30 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-R
 Ligand Interaction
IRI
Query on IRI

Download SDF File 
Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
SR
Query on SR

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.091α = 90.00
b = 49.091β = 90.00
c = 246.341γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM022778

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Refinement description