3G9C

Crystal structure of the product Bacillus anthracis glmS ribozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme

Cochrane, J.C.Lipchock, S.V.Smith, K.D.Strobel, S.A.

(2009) Biochemistry 48: 3239-3246

  • DOI: 10.1021/bi802069p
  • Primary Citation of Related Structures:  
    3G9C, 3G8T, 3G96, 3G8S, 3L3C

  • PubMed Abstract: 
  • The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, ...

    The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AABCD98Homo 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
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')E, F, G, H11synthetic construct
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    GLMS RIBOZYMEP, Q, R, S141synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GLP
    Query on GLP

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Free: 0.307 
    • R-Value Work: 0.246 
    • R-Value Observed: 0.249 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 49.586α = 90
    b = 229.827β = 90.16
    c = 101.75γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection
    HKL-2000data reduction
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2009-11-03
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2017-11-01
      Changes: Refinement description
    • Version 1.3: 2018-04-04
      Changes: Data collection, Database references
    • Version 1.4: 2018-04-11
      Changes: Data collection, Source and taxonomy
    • Version 1.5: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Data collection, Derived calculations, Structure summary