3OH9

AlkA Undamaged DNA Complex: Interrogation of a T:A base pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.802 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Escherichia coli AlkA in Complex with Undamaged DNA.

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

(2010) J.Biol.Chem. 285: 35783-35791

  • DOI: 10.1074/jbc.M110.155663
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction ...

    Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction between these proteins and undamaged DNA. Here we report the crystal structures of the DNA glycosylase AlkA in complex with undamaged DNA. The structures revealed a recognition mode in which the DNA is nearly straight, with no amino acid side chains inserted into the duplex, and the target base pair is fully intrahelical. A comparison of the present structures with that of AlkA recognizing an extrahelical lesion revealed conformational changes in both the DNA and protein as the glycosylase transitions from the interrogation of undamaged DNA to catalysis of nucleobase excision. Modeling studies with the cytotoxic lesion 3-methyladenine and accompanying biochemical experiments suggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence of lesions.


    Organizational Affiliation

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-3-methyladenine glycosylase 2
A
289Escherichia coli (strain K12)Mutation(s): 1 
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
5'-D(*GP*GP*CP*AP*TP*TP*CP*AP*TP*GP*T)-3'B11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*CP*AP*(BRU)P*GP*AP*AP*(BRU)P*GP*CP*C)-3'C11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
C
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.802 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.900α = 90.00
b = 139.900β = 90.00
c = 91.100γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CNSphasing
SCALEPACKdata scaling
ADSCdata collection
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance