124D

STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE PURE RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a DNA:RNA Hybrid Duplex. Why Rnase H Does not Cleave Pure RNA

Fedoroff, O.Y.Salazar, M.Reid, B.R.

(1993) J.Mol.Biol. 233: 509-523


  • PubMed Abstract: 
  • The solution structure of the DNA:RNA hybrid duplex d(GTCACATG):r(caugugac) has been determined by means of two-dimensional nuclear Overhauser effect (2D-NOE) spectra, restrained molecular dynamics and full-relaxation matrix stimulation of the 2D-NOE ...

    The solution structure of the DNA:RNA hybrid duplex d(GTCACATG):r(caugugac) has been determined by means of two-dimensional nuclear Overhauser effect (2D-NOE) spectra, restrained molecular dynamics and full-relaxation matrix stimulation of the 2D-NOE spectra. The DNA:RNA hybrid duplex assumes neither an A-form nor a B-form structure in solution, but an intermediate heteromerous duplex structure. The sugars of the RNA strand have a normal N-type C3'-endo conformation, but the DNA strand sugars have neither N-type nor S-type conformations; instead, they have an unexpected intermediate O4'-endo conformation. The negative x-displacement, as well as the small rise and positive inclination of the base-pairs, resembles A-form morphology but the minor groove width is intermediate between that of A-form and B-form duplexes. Both the DNA and RNA strands show prominent sequence-dependent variations in their helical parameters. Combined analysis of NOE and J-coupling data indicates that the DNA sugars are not in a dynamical two-state equilibrium. The detailed three-dimensional structure of this DNA:RNA hybrid molecule leads to a proposed model for its interaction with RNase H. Several specific structural features of the enzyme complexed with the hybrid duplex appear to explain the mechanism whereby RNase H discriminates between DNA:RNA hybrid duplexes and pure RNA:RNA duplexes.


    Related Citations: 
    • The DNA Strand in DNA-RNA Hybrid Duplexes is Neither B-Form Nor A-Form in Solution
      Salazar, M.,Fedoroff, O.Y.,Miller, J.M.,Ribeiro, N.S.,Reid, B.R.
      (1993) Biochemistry 32: 4207


    Organizational Affiliation

    Department of Chemistry, University of Washington, Seattle 98195.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*G)-3')A8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*AP*UP*GP*UP*GP*AP*C)-3')B8N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance