1B5K

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct.

Cullinan, D.Korobka, A.Grollman, A.P.Patel, D.J.Eisenberg, M.De Los Santos, C.

(1996) Biochemistry 35: 13319-13327

  • DOI: 10.1021/bi9605705

  • PubMed Abstract: 
  • The exocyclic 3,N4-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-epsilon C-C-A-T-G-C).d (G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high-resolution proton NMR s ...

    The exocyclic 3,N4-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-epsilon C-C-A-T-G-C).d (G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high-resolution proton NMR spectroscopy and molecular dynamics simulations. The experimental data indicate that the oligodeoxynucleotide duplex adopts a right-handed helical structure with sugar puckers in the C2'-endo/C3'-exo range and Watson-Crick hydrogen bond alignments for all base pairs. NOE connectivities established a syn orientation for the glycosidic torsion angle of the exocyclic adduct. Restrained molecular dynamics simulations, using the full relaxation matrix approach, produced a three-dimensional model in agreement with the experimental data. The structure shows only minor perturbations in the sugar-phosphate backbone and a 27 degrees bend of the helical axis at the lesion site. On the refined model a well-formed hydrogen bond between T (N3H) and epsilon C(N4) stabilizes the epsilon C(syn).T(anti) base pair alignment, reflecting the preference of the adduct for the syn orientation. Furthermore, the epsilon C(syn).T(anti) base pair stacks with flanking base pairs. We discuss a correlation between the mutagenic properties of the adduct and the three-dimensional structure of the epsilon C.dA and epsilon C.T duplexes.


    Organizational Affiliation

    Department of Pharmacological Sciences, State University of New York at Stony Brook 11794-8651, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*CP*EDCP*CP*AP*TP*GP*C)-3')A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3')B11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
EDC
Query on EDC
A
DNA LINKINGC11 H14 N3 O7 P

--

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: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-01-18
    Type: Atomic model
  • Version 1.4: 2017-02-01
    Type: Structure summary