2L5Z

NMR structure of the A730 loop of the Neurospora VS ribozyme

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.2 of the entry. See complete history. 


Literature

NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site.

Desjardins, G., Bonneau, E., Girard, N., Boisbouvier, J., Legault, P.

(2011) Nucleic Acids Res 39: 4427-4437

  • DOI: 10.1093/nar/gkq1244
  • Primary Citation of Related Structures:  
    2L5Z

  • PubMed Abstract: 

    • The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem-loop VI fragment containing the A730 internal loop, which forms part of the active site ...

    The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem-loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson-Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme.

    Related Citations: 
    • NMR Structure of the A730 loop of the Neurospora VS Ribozyme: Insights into the Formation of the Active Site
      Desjardins, G., Bonneau, E., Girard, N., Boisbouvier, J., Legault, P.
      () To be published --: --
    Organizational Affiliation: 

    Département de Biochimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (26-MER)A 26Neurospora
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2L5Z Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-05
    Changes: Data collection, Database references, Other