3SD3

The structure of the tetrahydrofolate riboswitch containing a U25C mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.

Trausch, J.J.Ceres, P.Reyes, F.E.Batey, R.T.

(2011) Structure 19: 1413-1423

  • DOI: 10.1016/j.str.2011.06.019
  • Primary Citation of Related Structures:  
  • Also Cited By: 4LW0, 4LVZ, 4LVY, 4LVX, 4LVW, 4LVV

  • PubMed Abstract: 
  • Transport and biosynthesis of folate and its derivatives are frequently controlled by the tetrahydrofolate (THF) riboswitch in Firmicutes. We have solved the crystal structure of the THF riboswitch aptamer in complex with folinic acid, a THF analog. ...

    Transport and biosynthesis of folate and its derivatives are frequently controlled by the tetrahydrofolate (THF) riboswitch in Firmicutes. We have solved the crystal structure of the THF riboswitch aptamer in complex with folinic acid, a THF analog. Uniquely, this structure reveals two molecules of folinic acid binding to a single structured domain. These two sites interact with ligand in a similar fashion, primarily through recognition of the reduced pterin moiety. 7-deazaguanine, a soluble analog of guanine, binds the riboswitch with nearly the same affinity as its natural effector. However, 7-deazaguanine effects transcriptional termination to a substantially lesser degree than folinic acid, suggesting that the cellular guanine pool does not act upon the THF riboswitch. Under physiological conditions the ligands display strong cooperative binding, with one of the two sites playing a greater role in eliciting the regulatory response, which suggests that the second site may play another functional role.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, CO 80309-0215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Tetrahydrofolate riboswitchA89N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFO
Query on FFO

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Download CCD File 
A
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
[6S]-5-FORMYL-TETRAHYDROFOLATE; 6S-FOLINIC ACID
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
 Ligand Interaction
IRI
Query on IRI

Download SDF File 
Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FOZKd: 18000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 27.520α = 90.00
b = 68.590β = 90.00
c = 158.080γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
SCALAdata scaling
XSCALEdata scaling
BOSdata collection
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-09-28
    Type: Database references
  • Version 1.2: 2011-11-02
    Type: Database references
  • Version 2.0: 2019-11-20
    Type: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary