1MPG

3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the excision repair of alkylation-damaged DNA.

Labahn, J.Scharer, O.D.Long, A.Ezaz-Nikpay, K.Verdine, G.L.Ellenberger, T.E.

(1996) Cell 86: 321-329


  • PubMed Abstract: 
  • Base-excision DNA repair proteins that target alkylation damage act on a variety of seemingly dissimilar adducts, yet fail to recognize other closely related lesions. The 1.8 A crystal structure of the monofunctional DNA glycosylase AlkA (E. coli 3-m ...

    Base-excision DNA repair proteins that target alkylation damage act on a variety of seemingly dissimilar adducts, yet fail to recognize other closely related lesions. The 1.8 A crystal structure of the monofunctional DNA glycosylase AlkA (E. coli 3-methyladenine-DNA glycosylase II) reveals a large hydrophobic cleft unusually rich in aromatic residues. An Asp residue projecting into this cleft is essential for catalysis, and it governs binding specificity for mechanism-based inhibitors. We propose that AlkA recognizes electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. Remarkably, AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III, suggesting the two may employ fundamentally related mechanisms for base excision.


    Related Citations: 
    • Three-Dimensional Structure of a DNA Repair Enzyme, 3-Methyladenine DNA Glycosylase II, from Escherichia Coli
      Yamagata, Y.,Kato, M.,Odawara, K.,Tokuno, Y.,Nakashima, Y.,Matsushima, N.,Yasumura, K.,Tomita, K.I.,Ihara, K.,Fujii, Y.,Nakabeppu, Y.,Sekiguchi, M.,Fujii, S.
      (1996) Cell 86: 311


    Organizational Affiliation

    Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-METHYLADENINE DNA GLYCOSYLASE II
A, B
282Escherichia coli (strain K12)Gene Names: alkA (aidA)
EC: 3.2.2.21
Find proteins for P04395 (Escherichia coli (strain K12))
Go to UniProtKB:  P04395
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
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: 1.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.080α = 90.00
b = 75.770β = 109.94
c = 60.920γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance