3GO8

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-loop deletion complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report



Literature

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme

Qi, Y.Spong, M.C.Nam, K.Banerjee, A.Jiralerspong, S.Karplus, M.Verdine, G.L.

(2009) Nature 462: 762-766

  • DOI: 10.1038/nature08561
  • Primary Citation of Related Structures:  
    3GO8, 3GP1, 3GQ5, 3GPU, 3GPX, 3GPY, 3GPP, 3GQ3, 3GQ4

  • PubMed Abstract: 
  • How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stag ...

    How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine (oxoG), nested within a DNA duplex. Three structures of intrahelical oxoG-encounter complexes are compared with sequence-matched structures containing a normal G base in place of an oxoG lesion. Although the protein-DNA interfaces in the matched complexes differ by only two atoms-those that distinguish oxoG from G-their pronounced structural differences indicate that MutM can detect a lesion in DNA even at the earliest stages of encounter. All-atom computer simulations show the pathway by which encounter of the enzyme with the lesion causes extrusion from the DNA duplex, and they elucidate the critical free energy difference between oxoG and G along the extrusion pathway.


    Organizational Affiliation

    Graduate Program in Biophysics, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Formamidopyrimidine-DNA glycosylaseA257Geobacillus stearothermophilusMutation(s): 1 
Gene Names: mutMfpg
EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for P84131 (Geobacillus stearothermophilus)
Explore P84131 
Go to UniProtKB:  P84131
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3'C16synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3'B16synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download CCD File 
      A
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.89 Å
      • R-Value Free: 0.218 
      • R-Value Work: 0.185 
      • R-Value Observed: 0.187 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 45.244α = 90
      b = 92.655β = 90
      c = 105.246γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2009-12-15
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Advisory, Version format compliance
      • Version 1.2: 2017-11-01
        Changes: Refinement description
      • Version 2.0: 2019-02-06
        Changes: Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary