3B4C

T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 

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This is version 1.3 of the entry. See complete history. 


Literature

Essential Role of an Active-Site Guanine in glmS Ribozyme Catalysis.

Klein, D.J., Been, M.D., Ferre-D'Amare, A.R.

(2007) J Am Chem Soc 129: 14858-14859

  • DOI: https://doi.org/10.1021/ja0768441
  • Primary Citation of Related Structures:  
    3B4A, 3B4B, 3B4C

  • PubMed Abstract: 

    The glmS ribozyme is a catalytic riboswitch that is activated for endonucleolytic cleavage by the coenzyme glucosamine-6-phosphate. Using kinetic assays and X-ray crystallography, we identify an active-site mutation of a conserved guanine that abolishes catalysis without perturbing coenzyme binding. Our results provide evidence that coenzyme function requires a specific nucleobase to interact with the nucleophile of the cleavage reaction.

    • Organizational Affiliation: 

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.


Macromolecules
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Entity ID: 1
MoleculeChains LengthOrganismImage
glmS ribozyme substrate with a 2'5'-phosphodiester linkage26Caldanaerobacter subterraneus subsp. tengcongensis
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
glmS ribozyme RNA125Caldanaerobacter subterraneus subsp. tengcongensis
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.3α = 90
b = 40.4β = 90
c = 77.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Structure summary