1RRQ

MutY adenine glycosylase in complex with DNA containing an A:oxoG pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase

Fromme, J.C.Banerjee, A.Huang, S.J.Verdine, G.L.

(2004) Nature 427: 652-656

  • DOI: 10.1038/nature02306
  • Primary Citation of Related Structures:  
    1RRS, 1RRQ, 1VRL

  • PubMed Abstract: 
  • The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resu ...

    The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MutY A369Geobacillus stearothermophilusMutation(s): 0 
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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'B11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3'C11N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SF4
      Query on SF4

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

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.22 Å
      • R-Value Free: 0.262 
      • R-Value Work: 0.226 
      • R-Value Observed: 0.226 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 37.763α = 90
      b = 85.699β = 90
      c = 142.088γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      HKL-2000data reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-02-17
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance