3SAU

MUTM Interrogation complex 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 

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.USA 109: 1086-1091

  • DOI: 10.1073/pnas.1111237108
  • Primary Citation of Related Structures:  

  • 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 pr ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GLYCOSYLASE
A
273Geobacillus stearothermophilusMutation(s): 1 
Gene Names: mutM (fpg)
EC: 3.2.2.23
Find proteins for P84131 (Geobacillus stearothermophilus)
Go to UniProtKB:  P84131
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3'B16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TX2
Query on TX2
C
DNA LINKINGC12 H20 N3 O7 P S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.423α = 90.00
b = 93.436β = 90.00
c = 104.920γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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