2P7E

Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization

Torelli, A.T.Krucinska, J.Wedekind, J.E.

(2007) RNA 13: 1052-1070

  • DOI: https://doi.org/10.1261/rna.510807
  • Primary Citation of Related Structures:  
    2P7D, 2P7E, 2P7F

  • PubMed Abstract: 

    The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Rochester, NY 14642, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5' substrate strand, pentameric fragment5N/A
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Ribozyme strand I13N/A
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
Ribozyme strand II17N/A
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
Ribozyme strand III19N/A
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
3' substrate strand, octameric fragmentE [auth P]8N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.1α = 90
b = 94.1β = 90
c = 132.4γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description