6P2H

Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches

  • Classification: RNA
  • Organism(s): synthetic construct

  • Deposited: 2019-05-21 Released: 2019-10-23 
  • Deposition Author(s): Matyjasik, M.M., Batey, R.T.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches.

Matyjasik, M.M.Batey, R.T.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz839

  • PubMed Abstract: 
  • A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the regulatory molecule of the parental class. Within the guanine/adenine class, seven groups of RNAs were identified that deviate fro ...

    A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the regulatory molecule of the parental class. Within the guanine/adenine class, seven groups of RNAs were identified that deviate from the consensus sequence at one or more of three positions directly involved purine nucleobase recognition, one of which was validated as a second class of 2'-deoxyguanosine riboswitch (called 2'-dG-II). To understand how 2'-dG-II riboswitches recognize their cognate ligand and how they differ from a previously identified class of 2'-deoxyguanosine binding riboswitches, we have solved the crystal structure of a 2'-dG-II aptamer domain bound to 2'-deoxyguanosine. This structure reveals a global architecture similar to other members of the purine riboswitch family, but contains key differences within the ligand binding core. Defining the 2'-dG-II riboswitches is a two-nucleotide insertion in the three-way junction that promotes novel base-base interactions. Unlike 2'-dG-I riboswitches, the 2'-dG-II class only requires local changes to the ligand binding pocket of the guanine/adenine class to achieve a change in ligand preference. Notably, members of the 2'-dG-II family have variable ability to discriminate between 2'-deoxyguanosine and riboguanosine, suggesting that a subset of 2'-dG-II riboswitches may bind either molecule to regulate gene expression.


    Organizational Affiliation

    Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (69-MER)A69synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNG
Query on GNG

Download SDF File 
Download CCD File 
A
2'-DEOXY-GUANOSINE
C10 H13 N5 O4
YKBGVTZYEHREMT-KVQBGUIXSA-N
 Ligand Interaction
NCO
Query on NCO

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Download CCD File 
A
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.805α = 90.00
b = 91.805β = 90.00
c = 77.756γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM073850

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release