3SKW

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cesium soak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.

Pikovskaya, O.Polonskaia, A.Patel, D.J.Serganov, A.

(2011) Nat.Chem.Biol. 7: 748-755

  • DOI: 10.1038/nchembio.631
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Purine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles t ...

    Purine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles that define dG selectivity, we determined crystal structures of the natural Mesoplasma florum riboswitch bound to cognate dG as well as to noncognate guanosine, deoxyguanosine monophosphate and guanosine monophosphate. Comparison with related purine riboswitch structures reveals that the dG riboswitch achieves its specificity through modification of key interactions involving the nucleobase and rearrangement of the ligand-binding pocket to accommodate the additional sugar moiety. In addition, we observe new conformational changes beyond the junctional binding pocket extending as far as peripheral loop-loop interactions. It appears that re-engineering riboswitch scaffolds will require consideration of selectivity features dispersed throughout the riboswitch tertiary fold, and structure-guided drug design efforts targeted to junctional RNA scaffolds need to be addressed within such an expanded framework.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (66-MER)A,B66N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNG
Query on GNG

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

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

Download SDF File 
Download CCD File 
A
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
A, B
RNA LINKINGC9 H13 N3 O10 P2C
GTP
Query on GTP
A, B
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.376α = 90.00
b = 35.414β = 95.18
c = 119.269γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
CBASSdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references