4NYA

Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.

Warner, K.D.Homan, P.Weeks, K.M.Smith, A.G.Abell, C.Ferre-D'Amare, A.R.

(2014) Chem.Biol. 21: 591-595

  • DOI: 10.1016/j.chembiol.2014.03.007
  • Primary Citation of Related Structures:  4NYB, 4NYC, 4NYD, 4NYG

  • PubMed Abstract: 
  • Thiamine pyrophosphate (TPP) riboswitches regulate essential genes in bacteria by changing conformation upon binding intracellular TPP. Previous studies using fragment-based approaches identified small molecule "fragments" that bind this gene-regulat ...

    Thiamine pyrophosphate (TPP) riboswitches regulate essential genes in bacteria by changing conformation upon binding intracellular TPP. Previous studies using fragment-based approaches identified small molecule "fragments" that bind this gene-regulatory mRNA domain. Crystallographic studies now show that, despite having micromolar Kds, four different fragments bind the TPP riboswitch site-specifically, occupying the pocket that recognizes the aminopyrimidine of TPP. Unexpectedly, the unoccupied site that would recognize the pyrophosphate of TPP rearranges into a structure distinct from that of the cognate complex. This idiosyncratic fragment-induced conformation, also characterized by small-angle X-ray scattering and chemical probing, represents a possible mechanism for adventitious ligand discrimination by the riboswitch, and suggests that off-pathway conformations of RNAs can be targeted for drug development. Our structures, together with previous screening studies, demonstrate the feasibility of fragment-based drug discovery against RNA targets.


    Organizational Affiliation

    National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
thiM TPP riboswitchA,B80Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2QB
Query on 2QB

Download SDF File 
Download CCD File 
A, B
5-(azidomethyl)-2-methylpyrimidin-4-amine
C6 H8 N6
HRZOZFYDZBEQQQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 149.730α = 90.00
b = 29.890β = 93.94
c = 95.430γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release