3JR5

MutM lesion recognition control complex with N174C crosslinking site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.

Qi, Y.Spong, M.C.Nam, K.Karplus, M.Verdine, G.L.

(2010) J Biol Chem 285: 1468-1478

  • DOI: 10.1074/jbc.M109.069799
  • Primary Citation of Related Structures:  
    3JR4, 3JR5

  • PubMed Abstract: 
  • MutM, a bacterial DNA glycosylase, protects genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions, thereby initiating base excision DNA repair. The process of searching for and locating oxoG lesions is especially challeng ...

    MutM, a bacterial DNA glycosylase, protects genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions, thereby initiating base excision DNA repair. The process of searching for and locating oxoG lesions is especially challenging, because of the close structural resemblance of oxoG to its million-fold more abundant progenitor, G. Extrusion of the target nucleobase from the DNA double helix to an extrahelical position is an essential step in lesion recognition and catalysis by MutM. Although the interactions between the extruded oxoG and the active site of MutM have been well characterized, little is known in structural detail regarding the interrogation of extruded normal DNA bases by MutM. Here we report the capture and structural elucidation of a complex in which MutM is attempting to present an undamaged G to its active site. The structure of this MutM-extrahelical G complex provides insights into the mechanism MutM employs to discriminate against extrahelical normal DNA bases and into the base extrusion process in general.


    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
DNA glycosylase A273Geobacillus stearothermophilusMutation(s): 1 
Gene Names: mutMfpg
EC: 4.2.99.18 (PDB Primary Data), 3.2.2.23 (UniProt)
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: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')B16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(OGX)P*AP*GP*TP*CP*TP*AP*CP*C)-3')C16N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.185 
      • R-Value Work: 0.165 
      • R-Value Observed: 0.166 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 45.343α = 90
      b = 95.377β = 90
      c = 102.482γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2009-11-03
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Non-polymer description, Version format compliance
      • Version 1.2: 2017-11-01
        Changes: Refinement description