1FKY

NMR STUDY OF B-DNA CONTAINING A MISMATCHED BASE PAIR IN THE 29-39 K-RAS GENE SEQUENCE: CC CT C+C C+T, 2 STRUCTURES


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

Solution structure as a function of pH of two central mismatches, C . T and C . C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics.

Boulard, Y.Cognet, J.A.Fazakerley, G.V.

(1997) J.Mol.Biol. 268: 331-347

  • DOI: 10.1006/jmbi.1997.0975
  • Primary Citation of Related Structures:  1FKZ

  • PubMed Abstract: 
  • The DNA duplexes 5' d(GCCACCAGCTC) x d(GAGCTXGTGGC), where the base X is either cytosine or thymine, have been studied by one and two-dimensional nuclear magnetic resonance, energy minimization and molecular dynamics. The sequence studied corresponds ...

    The DNA duplexes 5' d(GCCACCAGCTC) x d(GAGCTXGTGGC), where the base X is either cytosine or thymine, have been studied by one and two-dimensional nuclear magnetic resonance, energy minimization and molecular dynamics. The sequence studied corresponds to the region 29 to 39 of the K-ras gene and is a hot spot for mutations. The results show that both duplexes adopt a globally B-DNA-type structure. For the C x C mismatch, we observe a structural change as a function of pH with an apparent pK of 6.95. The neutral species has only one hydrogen bond between the two bases but shows two families of wobble structures where one base or the other is displaced in the major groove. The protonated species has two hydrogen bonds and two structures but of unequal populations. In both systems, the sugar puckers remain predominantly C2'-endo and no significant changes in the backbone structure are observed. The neutral C . T mismatch is stabilized by two hydrogen bonds but, surprisingly, it can also be protonated, although the apparent pK is much lower, 5.65. In this case, protonation does not result in an additional hydrogen bond but must be due to better base-stacking interactions for C+ x T. The NMR data show that the environment of the T imino proton is very similar for C x T and C+ x T, although the hydrogen bond acceptor would be expected to be a nitrogen atom in the former case and an oxygen atom in the latter. We propose that for both structures there is an intervening water molecule which in addition reduces backbone strain. We have also measured the fluctuations during molecular dynamics runs in these mismatches. All are greater than for Watson-Crick base-pairs and the C x C mismatch shows very pronounced mobility.


    Related Citations: 
    • Solution Structure of Two Mismatches A.A and T.T in the K-Ras Gene Context by Nuclear Magnetic Resonance and Molecular Dynamics
      Gervais, V.,Cognet, J.A.,Le Bret, M.,Sowers, L.C.,Fazakerley, G.V.
      (1995) Eur.J.Biochem. 228: 279
    • Solution Structure of an Oncogenic DNA Duplex, the K-Ras Gene and the Sequence Containing a Central C.A or A.G Mismatch as a Function of Ph: Nuclear Magnetic Resonance and Molecular Dynamics Studies
      Boulard, Y.,Cognet, J.A.,Gabarro-Arpa, J.,Le Bret, M.,Carbonnaux, C.,Fazakerley, G.V.
      (1995) J.Mol.Biol. 246: 194
    • Helical Parameters, Fluctuations, Alternative Hydrogen Bonding, and Bending in Oligonucleotides Containing a Mismatched Base-Pair by Noesy Distance Restrained and Distance Free Molecular Dynamics
      Cognet, J.A.,Boulard, Y.,Fazakerley, G.V.
      (1995) J.Mol.Biol. 246: 209


    Organizational Affiliation

    CEA, D├ępartement de Biologie Cellulaire et Mol├ęculaire, Centre d'Etudes de Saclay, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*AP*CP*CP*AP*GP*CP*TP*C)-3')A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*CP*TP*TP*GP*TP*GP*GP*C)-3')B11N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance