6DMD

ppGpp Riboswitch bound to ppGpp, manganese chloride structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.

Peselis, A.Serganov, A.

(2018) Nat Chem Biol 14: 887-894

  • DOI: 10.1038/s41589-018-0114-4
  • Primary Citation of Related Structures:  
    6DLQ, 6DLS, 6DLR, 6DLT, 6DMD, 6DMC, 6DME, 6DNR

  • PubMed Abstract: 
  • The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures ...

    The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg 2+ -mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA. alexander.serganov@nyumc.org.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
ppGpp RiboswitchA, B102Sulfobacillus acidophilus DSM 10332
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4P
Query on G4P

Download CCD File 
A, B
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.741α = 90
b = 49.595β = 97.29
c = 79.365γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM112940
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31GM119357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM88118

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Advisory, Author supporting evidence