5CL4

Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (71% substrate/29% product at 24 hours)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.

Mullins, E.A.Shi, R.Parsons, Z.D.Yuen, P.K.David, S.S.Igarashi, Y.Eichman, B.F.

(2015) Nature 527: 254-258

  • DOI: 10.1038/nature15728
  • Primary Citation of Related Structures:  
    5CL3, 5CL4, 5CL5, 5CL6, 5CL7, 5CL8, 5CL9, 5CLA, 5CLB, 5CLC, 5CLD, 5CLE

  • PubMed Abstract: 
  • Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research ...

    Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge-dipole and CH-π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.


    Organizational Affiliation

    Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AlkDA241Bacillus cereusMutation(s): 0 
Gene Names: IKE_03968
EC: 3.2.2
UniProt
Find proteins for Q816E8 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711))
Explore Q816E8 
Go to UniProtKB:  Q816E8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3')B12synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')C12synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      54K
      Query on 54K

      Download Ideal Coordinates CCD File 
      D [auth B]7-methyl-3H-imidazo[4,5-c]pyridin-4-amine
      C7 H8 N4
      VUSDRZRNZRBERR-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.87 Å
      • R-Value Free: 0.196 
      • R-Value Work: 0.153 
      • R-Value Observed: 0.155 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 38.247α = 90
      b = 93.558β = 112.74
      c = 47.976γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data scaling
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data reduction
      PHENIXphasing
      Cootmodel building

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Science Foundation (NSF, United States)United StatesMCB-1122098

      Revision History  (Full details and data files)

      • Version 1.0: 2015-10-28
        Type: Initial release
      • Version 1.1: 2015-11-18
        Changes: Database references
      • Version 1.2: 2015-11-25
        Changes: Database references
      • Version 1.3: 2017-09-06
        Changes: Author supporting evidence, Database references, Derived calculations
      • Version 1.4: 2019-11-27
        Changes: Author supporting evidence