4MEG

In vitro evolved glmS ribozyme triple mutant, magnesium ion complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence.

Lau, M.W.Ferre-D'Amare, A.R.

(2013) Nat.Chem.Biol. 9: 805-810

  • DOI: 10.1038/nchembio.1360
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uniquely among known ribozymes, the glmS ribozyme-riboswitch requires a small-molecule coenzyme, glucosamine-6-phosphate (GlcN6P). Although consistent with its gene-regulatory function, the use of GlcN6P is unexpected because all of the other charact ...

    Uniquely among known ribozymes, the glmS ribozyme-riboswitch requires a small-molecule coenzyme, glucosamine-6-phosphate (GlcN6P). Although consistent with its gene-regulatory function, the use of GlcN6P is unexpected because all of the other characterized self-cleaving ribozymes use RNA functional groups or divalent cations for catalysis. To determine what active site features make this ribozyme reliant on GlcN6P and to evaluate whether it might have evolved from a coenzyme-independent ancestor, we isolated a GlcN6P-independent variant through in vitro selection. Three active site mutations suffice to generate a highly reactive RNA that adopts the wild-type fold but uses divalent cations for catalysis and is insensitive to GlcN6P. Biochemical and crystallographic comparisons of wild-type and mutant ribozymes show that a handful of functional groups fine-tune the RNA to be either coenzyme or cation dependent. These results indicate that a few mutations can confer new biochemical activities on structured RNAs. Thus, families of structurally related ribozymes with divergent function may exist.


    Organizational Affiliation

    National Heart, Lung and Blood Institute, Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
glmS triple mutant ribozymeA27N/A
Entity ID: 2
MoleculeChainsLengthOrganism
(121-MER) ribozymeB126N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 166.900α = 90.00
b = 40.400β = 90.00
c = 73.600γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references