3SAT

MUTM Slanted complex 6 with R112A mutation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Strandwise translocation of a DNA glycosylase on undamaged DNA.

Qi, Y., Nam, K., Spong, M.C., Banerjee, A., Sung, R.J., Zhang, M., Karplus, M., Verdine, G.L.

(2012) Proc Natl Acad Sci U S A 109: 1086-1091

  • DOI: 10.1073/pnas.1111237108
  • Primary Citation of Related Structures:  
    3SAR, 3SAS, 3SAT, 3SAU, 3SAV, 3SAW, 3SBJ

  • PubMed Abstract: 

    • Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search proces ...

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

    Organizational Affiliation: 

    Program in Biophysics, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA GLYCOSYLASE A273Geobacillus stearothermophilusMutation(s): 2 
Gene Names: mutM, fpg
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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*GP*G*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3'B16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*CP*GP*T*CP*CP*TP*GP*GP*(TX2) P*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: 2.15 Å
      • R-Value Free: 0.225 
      • R-Value Work: 0.187 
      • R-Value Observed: 0.189 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 45.487α = 90
      b = 97.574β = 90
      c = 102.371γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      • Deposited Date: 2011-06-03 
      • Released Date: 2012-01-11 
        • Deposition Author(s): Qi, Y., Verdine, G.L.

      Revision History 

      • Version 1.0: 2012-01-11
        Type: Initial release
      • Version 1.1: 2012-02-22
        Changes: Database references
      • Version 1.2: 2017-11-08
        Changes: Refinement description
      • Version 1.3: 2019-07-17
        Changes: Data collection, Derived calculations, Refinement description