4HQI

Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.

Kowal, E.A.Lad, R.R.Pallan, P.S.Dhummakupt, E.Wawrzak, Z.Egli, M.Sturla, S.J.Stone, M.P.

(2013) Nucleic Acids Res. 41: 7566-7576

  • DOI: 10.1093/nar/gkt488
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O(6)-benzyl-2'-deoxyguanosine nucleoside (O(6)-Bn-dG), formed by exposure to N-b ...

    The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O(6)-benzyl-2'-deoxyguanosine nucleoside (O(6)-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O(6)-Bn-dG and dG in DNA. The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G(4) has been replaced by O(6)-Bn-dG and cytosine C(9) has been replaced with dPer to form the modified O(6)-Bn-dG:dPer (DDD-XY) duplex [5'-d(C(1)G(2)C(3)X(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 (X = O(6)-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O(6)-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O(6)-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C(9) is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.


    Organizational Affiliation

    Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Short modified nucleic acidsA,B12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
D3N
Query on D3N
A, B
DNA LINKINGC16 H17 N2 O7 P

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BZG
Query on BZG
A, B
DNA LINKINGC17 H20 N5 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 26.384α = 90.00
b = 36.774β = 90.00
c = 77.653γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data scaling
HKL-2000data reduction
MD2data collection
REFMACrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references