3CVS

Crystal Structure of an AlkA Host/Guest Complex 8oxoGuanine:Adenine Base Pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA.

Bowman, B.R.Lee, S.Wang, S.Verdine, G.L.

(2008) Structure 16: 1166-1174

  • DOI: 10.1016/j.str.2008.04.012
  • Primary Citation of Related Structures:  3CVT, 3CW7, 3CWA, 3CWS, 3CWT, 3CWU

  • PubMed Abstract: 
  • The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their ...

    The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences. The most definitive method of obtaining such structures, X-ray crystallography, is troublesome to employ owing to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we present a crystallization system that uses a protein, the DNA glycosylase AlkA, as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We demonstrate the use of this system to facilitate the rapid structure determination of DNA containing the lesion 8-oxoguanine in several different sequence contexts, and also deoxyinosine and 1,N(6)-ethenoadenine, each stabilized as the corresponding 2'-flouro analog. The structures of 8-oxoguanine provide a correct atomic-level view of this important endogenous lesion in DNA.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-3-methyladenine glycosylase 2
A, B, C, D
282Escherichia coli (strain K12)Gene Names: alkA (aidA)
EC: 3.2.2.21
Find proteins for P04395 (Escherichia coli (strain K12))
Go to UniProtKB:  P04395
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(8OG)P*DTP*DGP*DCP*DC)-3')E,G12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')F,H12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
E, G
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.174α = 90.00
b = 101.247β = 94.19
c = 102.917γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description