2F5N

MutM crosslinked to undamaged DNA sampling A:T base pair IC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a DNA glycosylase searching for lesions.

Banerjee, A.Santos, W.L.Verdine, G.L.

(2006) Science 311: 1153-1157

  • DOI: 10.1126/science.1120288
  • Primary Citation of Related Structures:  2F5O, 2F5P, 2F5Q, 2F5S

  • PubMed Abstract: 
  • DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) ...

    DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
formamidopyrimidine-DNA glycosidase
A
274Geobacillus stearothermophilusGene Names: mutM (fpg)
EC: 3.2.2.23
Find proteins for P84131 (Geobacillus stearothermophilus)
Go to UniProtKB:  P84131
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'B16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*CP*TP*AP*CP*C)-3'C16N/A
Small Molecules
Ligands 2 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.379α = 90.00
b = 92.947β = 90.00
c = 105.195γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2015-07-08
    Type: Structure summary