3GPY

Sequence-matched MutM Lesion Recognition Complex 3 (LRC3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.

Qi, Y.Spong, M.C.Nam, K.Banerjee, A.Jiralerspong, S.Karplus, M.Verdine, G.L.

(2009) Nature 462: 762-766

  • DOI: 10.1038/nature08561
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stag ...

    How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine (oxoG), nested within a DNA duplex. Three structures of intrahelical oxoG-encounter complexes are compared with sequence-matched structures containing a normal G base in place of an oxoG lesion. Although the protein-DNA interfaces in the matched complexes differ by only two atoms-those that distinguish oxoG from G-their pronounced structural differences indicate that MutM can detect a lesion in DNA even at the earliest stages of encounter. All-atom computer simulations show the pathway by which encounter of the enzyme with the lesion causes extrusion from the DNA duplex, and they elucidate the critical free energy difference between oxoG and G along the extrusion pathway.


    Organizational Affiliation

    Graduate Program in Biophysics, Harvard Medical School, Boston, Massachusetts 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
DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)-3')B16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*T*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*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
8OG
Query on 8OG
C
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.904α = 90.00
b = 95.207β = 90.00
c = 102.238γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-03-23 
  • Released Date: 2009-11-10 
  • Deposition Author(s): Qi, Y., Verdine, G.L.

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description