2NZ4

Structural investigation of the GlmS ribozyme bound to its catalytic cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    2NZ4

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U1 Small Nuclear Ribonucleoprotein AABCD94Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS  P09012
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    substrate strand RNA 13-merE, F, G, H13N/A
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    GlmS ribozymeP, Q, R, S141N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GLP
    Query on GLP

    Download CCD File 
    F, G, H, P
    2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
    C6 H14 N O8 P
    XHMJOUIAFHJHBW-UKFBFLRUSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    F, G, H, P, Q, R, S
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.269 
    • R-Value Work: 0.222 
    • R-Value Observed: 0.224 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 48.127α = 90
    b = 234.157β = 90.65
    c = 105.003γ = 90
    Software Package:
    Software NamePurpose
    CBASSdata collection
    SHARPphasing
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    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
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Non-polymer description, Version format compliance
    • Version 1.3: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Data collection, Derived calculations, Structure summary