3GS8

An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of an imino group indispensable for cleavage by a small ribozyme.

Spitale, R.C.Volpini, R.Heller, M.G.Krucinska, J.Cristalli, G.Wedekind, J.E.

(2009) J Am Chem Soc 131: 6093-6095

  • DOI: 10.1021/ja900450h
  • Primary Citation of Related Structures:  
    3GS8, 3GS1, 3GS5

  • PubMed Abstract: 
  • The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site ...

    The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.


    Organizational Affiliation

    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3')A14N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3')B12N/A
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')C17N/A
        Protein Feature View
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        • Reference Sequence
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
          MoleculeChainsLengthOrganismImage
          RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')D19N/A
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 3 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          S9L
          Query on S9L

          Download Ideal Coordinates CCD File 
          F [auth B]2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE
          C6 H15 O7 P
          CJHGCXGTUHBMMH-UHFFFAOYSA-N
           Ligand Interaction
          NCO
          Query on NCO

          Download Ideal Coordinates CCD File 
          G [auth B], H [auth C]COBALT HEXAMMINE(III)
          Co H18 N6
          DYLMFCCYOUSRTK-FGTKAUEHAT
           Ligand Interaction
          SO4
          Query on SO4

          Download Ideal Coordinates CCD File 
          E [auth A]SULFATE ION
          O4 S
          QAOWNCQODCNURD-UHFFFAOYSA-L
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 2.85 Å
          • R-Value Free: 0.254 
          • R-Value Work: 0.220 
          • R-Value Observed: 0.220 
          • Space Group: P 61 2 2
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 93.82α = 90
          b = 93.82β = 90
          c = 134.76γ = 120
          Software Package:
          Software NamePurpose
          CrystalCleardata collection
          CNSrefinement
          CrystalCleardata reduction
          CrystalCleardata scaling
          CNSphasing

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2009-04-21
            Type: Initial release
          • Version 1.1: 2011-07-13
            Changes: Version format compliance