4FEN

Crystal structure of the A24U/U25A/A46G mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch.

Stoddard, C.D.Widmann, J.Trausch, J.J.Marcano-Velazquez, J.G.Knight, R.Batey, R.T.

(2013) J.Mol.Biol. 425: 1596-1611

  • DOI: 10.1016/j.jmb.2013.02.023
  • Primary Citation of Related Structures:  4FEJ, 4FEL, 4FEO, 4FEP

  • PubMed Abstract: 
  • Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcriptio ...

    Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, 596 UCB, University of Colorado, Boulder, CO 80309-0596, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
A24U/U25A/A46G mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domainB67N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NCO
Query on NCO

Download SDF File 
Download CCD File 
B
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
HPA
Query on HPA

Download SDF File 
Download CCD File 
B
HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.689α = 90.00
b = 35.347β = 91.39
c = 41.388γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references
  • Version 1.2: 2013-05-22
    Type: Database references