1E4P

Structure of the ribozyme substrate hairpin of Neurospora VS RNA. A close look at the cleavage site

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

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


Literature

Structure of the Ribozyme Substrate Hairpin of Neurospora Vs RNA: A Close Look at the Cleavage Site

Michiels, P.J.A., Schouten, C.H.J., Hilbers, C.W., Heus, H.A.

(2000) RNA 6: 1821

  • DOI: 10.1017/s1355838200001394
  • Primary Citation of Related Structures:  
    1E4P

  • PubMed Abstract: 

    • The cleavage site of the Neurospora VS RNA ribozyme is located in a separate hairpin domain containing a hexanucleotide internal loop with an A-C mismatch and two adjacent G-A mismatches. The solution structure of the internal loop and helix la of the ribozyme substrate hairpin has been determined by nuclear magnetic resonance (NMR) spectroscopy ...

    The cleavage site of the Neurospora VS RNA ribozyme is located in a separate hairpin domain containing a hexanucleotide internal loop with an A-C mismatch and two adjacent G-A mismatches. The solution structure of the internal loop and helix la of the ribozyme substrate hairpin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The 2 nt in the internal loop, flanking the cleavage site, a guanine and adenine, are involved in two sheared G.A base pairs similar to the magnesium ion-binding site of the hammerhead ribozyme. Adjacent to the tandem G.A base pairs, the adenine and cytidine, which are important for cleavage, form a noncanonical wobble A+-C base pair. The dynamic properties of the internal loop and details of the high-resolution structure support the view that the hairpin structure represents a ground state, which has to undergo a conformational change prior to cleavage. Results of chemical modification and mutagenesis data of the Neurospora VS RNA ribozyme can be explained in context with the present three-dimensional structure.

    Organizational Affiliation: 

    NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*UP*GP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP* AP*GP*UP*CP*CP*GP*AP*GP*CP*GP*C)-3')A24Neurospora
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 
  • OLDERADO: 1E4P Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance