4ERL

Crystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Insights into the regulatory landscape of the lysine riboswitch.

Garst, A.D.Porter, E.B.Batey, R.T.

(2012) J Mol Biol 423: 17-33

  • DOI: https://doi.org/10.1016/j.jmb.2012.06.038
  • Primary Citation of Related Structures:  
    4ERJ, 4ERL

  • PubMed Abstract: 

    A prevalent means of regulating gene expression in bacteria is by riboswitches found within mRNA leader sequences. Like protein repressors, these RNA elements must bind an effector molecule with high specificity against a background of other cellular metabolites of similar chemical structure to elicit the appropriate regulatory response. Current crystal structures of the lysine riboswitch do not provide a complete understanding of selectivity as recognition is substantially mediated through main-chain atoms of the amino acid. Using a directed set of lysine analogs and other amino acids, we have determined the relative contributions of the polar functional groups to binding affinity and the regulatory response. Our results reveal that the lysine riboswitch has >1000-fold specificity for lysine over other amino acids. The aptamer is highly sensitive to the precise placement of the ε-amino group and relatively tolerant of alterations to the main-chain functional groups in order to achieve this specificity. At low nucleotide triphosphate (NTP) concentrations, we observe good agreement between the half-maximal regulatory activity (T(50)) and the affinity of the receptor for lysine (K(d)), as well as many of its analogs. However, above 400 μM [NTP], the concentration of lysine required to elicit transcription termination rises, moving into the riboswitch into a kinetic control regime. These data demonstrate that, under physiologically relevant conditions, riboswitches can integrate both effector and NTP concentrations to generate a regulatory response appropriate for global metabolic state of the cell.


  • Organizational Affiliation

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


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Lysine riboswitch RNA161Thermotoga maritima
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LYS PDBBind:  4ERL Kd: 5.70e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.878α = 90
b = 119.878β = 90
c = 58.743γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description