4G4O

MutM containing M77A mutation bound to oxoG-containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM.

Sung, R.J.Zhang, M.Qi, Y.Verdine, G.L.

(2013) J Biol Chem 288: 10012-10023

  • DOI: 10.1074/jbc.M112.415612
  • Primary Citation of Related Structures:  
    4G4N, 4G4O, 4G4Q, 4G4R

  • PubMed Abstract: 
  • MutM is a bacterial DNA glycosylase that serves as the first line of defense against the highly mutagenic 8-oxoguanine (oxoG) lesion, catalyzing glycosidic bond cleavage of oxoG to initiate base excision DNA repair. Previous work has shown that MutM actively interrogates DNA for the presence of an intrahelical oxoG lesion ...

    MutM is a bacterial DNA glycosylase that serves as the first line of defense against the highly mutagenic 8-oxoguanine (oxoG) lesion, catalyzing glycosidic bond cleavage of oxoG to initiate base excision DNA repair. Previous work has shown that MutM actively interrogates DNA for the presence of an intrahelical oxoG lesion. This interrogation process involves significant buckling and bending of the DNA to promote extrusion of oxoG from the duplex. Structural snapshots have revealed several different highly conserved residues that are prominently inserted into the duplex in the vicinity of the target oxoG before and after base extrusion has occurred. However, the roles of these helix-invading residues during the lesion recognition and base extrusion process remain unclear. In this study, we set out to probe the function of residues Phe(114) and Met(77) in oxoG recognition and repair. Here we report a detailed biochemical and structural characterization of MutM variants containing either a F114A or M77A mutation, both of which showed significant decreases in the efficiency of oxoG repair. These data reveal that Met(77) plays an important role in stabilizing the lesion-extruded conformation of the DNA. Phe(114), on the other hand, appears to destabilize the intrahelical state of the oxoG lesion, primarily by buckling the target base pair. We report the observation of a completely unexpected interaction state, in which the target base pair is ruptured but remains fully intrahelical; this structure vividly illustrates the disruptive influence of MutM on the target base pair.


    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: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Formamidopyrimidine-DNA glycosylaseA273Geobacillus stearothermophilusMutation(s): 2 
Gene Names: mutMfpg
EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for P84131 (Geobacillus stearothermophilus)
Explore P84131 
Go to UniProtKB:  P84131
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')B16N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*(TX2)P*CP*TP*AP*CP*C)-3')C16N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.95 Å
      • R-Value Free: 0.211 
      • R-Value Work: 0.175 
      • R-Value Observed: 0.177 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 45.188α = 90
      b = 93.541β = 90
      c = 104.65γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2013-02-20
        Type: Initial release
      • Version 1.1: 2013-02-27
        Changes: Database references
      • Version 1.2: 2013-04-24
        Changes: Database references