4LX5

X-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.

Robinson, C.J.Vincent, H.A.Wu, M.C.Lowe, P.T.Dunstan, M.S.Leys, D.Micklefield, J.

(2014) J.Am.Chem.Soc. 136: 10615-10624

  • DOI: 10.1021/ja502873j
  • Primary Citation of Related Structures:  4LX6

  • PubMed Abstract: 
  • Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and e ...

    Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tunable activation or repression of target gene expression, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, while providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes.


    Organizational Affiliation

    School of Chemistry, ‡Manchester Institute of Biotechnology and §Faculty of Life Sciences, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Mutated adenine riboswitch aptamerA71Vibrio vulnificus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
29G
Query on 29G

Download SDF File 
Download CCD File 
A
pyrimido[4,5-d]pyrimidine-2,4-diamine
C6 H6 N6
CEXXKZCAMOMPLI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.050α = 90.00
b = 149.710β = 90.00
c = 24.400γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
ADSCdata collection
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary