3UD3

The C92U mutant c-di-GMP-I riboswitch bound to pGpA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer.

Smith, K.D.Lipchock, S.V.Strobel, S.A.

(2012) Biochemistry 51: 425-432

  • DOI: 10.1021/bi2016662
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacte ...

    The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP 5 orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogues in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogues with properties desirable for use as chemical tools and potential therapeutics.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06520-8321, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
P
98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (92-MER)R92N/A
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*A)-3')A2N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
R
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.998α = 90.00
b = 45.391β = 94.98
c = 78.746γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CBASSdata collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-10-17
    Type: Database references