3G0Q

Crystal Structure of MutY bound to its inhibitor DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase.

Lee, S.Verdine, G.L.

(2009) Proc Natl Acad Sci U S A 106: 18497-18502

  • DOI: 10.1073/pnas.0902908106
  • Primary Citation of Related Structures:  
    3G0Q

  • PubMed Abstract: 
  • Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A.oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed ...

    Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A.oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed via the X-ray structure of a catalytically inactive mutant protein bound to an A:oxoG-containing DNA duplex. Although the structure revealed the substrate adenine to be, as expected, extruded from the DNA helix and inserted into an extrahelical active site pocket on the enzyme, the substrate adenine engaged in no direct contacts with active site residues. This feature was paradoxical, because other glycosylases have been observed to engage their substrates primarily through direct contacts. The lack of direct contacts in the case of MutY suggested that either MutY uses a distinctive logic for substrate recognition or that the X-ray structure had captured a noncatalytically competent state in lesion recognition. To gain further insight into this issue, we crystallized wild-type MutY bound to DNA containing a catalytically inactive analog of 2'-deoxyadenosine in which a single 2'-H atom was replaced by fluorine. The structure of this fluorinated lesion-recognition complex (FLRC) reveals the substrate adenine buried more deeply into the active site pocket than in the prior structure and now engaged in multiple direct hydrogen bonding and hydrophobic interactions. This structure appears to capture the catalytically competent state of adenine DNA glycosylases, and it suggests a catalytic mechanism for this class of enzymes, one in which general acid-catalyzed protonation of the nucleobase promotes glycosidic bond cleavage.


    Organizational Affiliation

    Departments of Stem Cell and Regenerative Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
A/G-specific adenine glycosylaseA352Geobacillus stearothermophilusMutation(s): 2 
Gene Names: mutY
EC: 3.2.2 (PDB Primary Data), 3.2.2.31 (UniProt)
Find proteins for P83847 (Geobacillus stearothermophilus)
Explore P83847 
Go to UniProtKB:  P83847
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*C)-3'B11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*TP*CP*CP*CP*AP*GP*TP*CP*TP*T)-3'C11N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SF4
      Query on SF4

      Download CCD File 
      A
      IRON/SULFUR CLUSTER
      Fe4 S4
      LJBDFODJNLIPKO-VKOJMFJBAC
       Ligand Interaction
      CA
      Query on CA

      Download CCD File 
      A
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.277 
      • R-Value Work: 0.246 
      • R-Value Observed: 0.246 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 37.7α = 90
      b = 85.9β = 90
      c = 142.1γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      HKL-2000data reduction
      CNSphasing

      Structure Validation

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      Entry History 

      Deposition Data

      • Deposited Date: 2009-01-28 
      • Released Date: 2009-11-17 
      • Deposition Author(s): Lee, S., Verdine, G.L.

      Revision History 

      • Version 1.0: 2009-11-17
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-11-01
        Changes: Refinement description
      • Version 1.3: 2018-01-24
        Changes: Structure summary