2NZ4

Structural investigation of the GlmS ribozyme bound to its catalytic cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.498 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor

Cochrane, J.C.Lipchock, S.V.Strobel, S.A.

(2007) Chem.Biol. 14: 97-105

  • DOI: 10.1016/j.chembiol.2006.12.005

  • PubMed Abstract: 
  • The GlmS riboswitch is located in the 5'-untranslated region of the gene encoding glucosamine-6-phosphate (GlcN6P) synthetase. The GlmS riboswitch is a ribozyme with activity triggered by binding of the metabolite GlcN6P. Presented here is the struct ...

    The GlmS riboswitch is located in the 5'-untranslated region of the gene encoding glucosamine-6-phosphate (GlcN6P) synthetase. The GlmS riboswitch is a ribozyme with activity triggered by binding of the metabolite GlcN6P. Presented here is the structure of the GlmS ribozyme (2.5 A resolution) with GlcN6P bound in the active site. The GlmS ribozyme adopts a compact double pseudoknot tertiary structure, with two closely packed helical stacks. Recognition of GlcN6P is achieved through coordination of the phosphate moiety by two hydrated magnesium ions as well as specific nucleobase contacts to the GlcN6P sugar ring. Comparison of this activator bound and the previously published apoenzyme complex supports a model in which GlcN6P does not induce a conformational change in the RNA, as is typical of other riboswitches, but instead functions as a catalytic cofactor for the reaction. This demonstrates that RNA, like protein enzymes, can employ the chemical diversity of small molecules to promote catalytic activity.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U1 Small Nuclear Ribonucleoprotein A
A, B, C, D
94Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
substrate strand RNA 13-merE,F,G,H13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
GlmS ribozymeP,Q,R,S141N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
F, G, H, P, Q, R, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GLP
Query on GLP

Download SDF File 
Download CCD File 
F, G, H, P
GLUCOSAMINE 6-PHOSPHATE
C6 H14 N O8 P
XHMJOUIAFHJHBW-UKFBFLRUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
E, F, G, H
RNA LINKINGC11 H16 N5 O7 PA
GTP
Query on GTP
P, Q, R, S
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.498 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.127α = 90.00
b = 234.157β = 90.65
c = 105.003γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
CBASSdata collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-22 
  • Released Date: 2007-01-16 
  • Deposition Author(s): Cochrane, J.C.

Revision History 

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance