3OGD

AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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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:  
    3OGD, 3OH6, 3OH9

  • 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 between these proteins and undamaged DNA ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-3-methyladenine glycosylase 2 A289Escherichia coli K-12Mutation(s): 1 
Gene Names: aidA, alkA, b2068, JW2053
EC: 3.2.2.21
Find proteins for P04395 (Escherichia coli (strain K12))
Explore P04395 
Go to UniProtKB:  P04395
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3'B9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3'C9N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.269 
      • R-Value Work: 0.215 
      • R-Value Observed: 0.218 
      • Space Group: I 41 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 139.7α = 90
      b = 139.7β = 90
      c = 95.3γ = 90
      Software Package:
      Software NamePurpose
      SCALEPACKdata scaling
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection
      HKL-2000data reduction
      CNSphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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