1PU8

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 1,N6-ethenoadenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases

Eichman, B.F.O'Rourke, E.J.Radicella, J.P.Ellenberger, T.

(2003) Embo J. 22: 4898-4909

  • DOI: 10.1093/emboj/cdg505
  • Primary Citation of Related Structures:  1PU6, 1PU7

  • PubMed Abstract: 
  • DNA glycosylases catalyze the excision of chemically modified bases from DNA. Although most glycosylases are specific to a particular base, the 3-methyladenine (m3A) DNA glycosylases include both highly specific enzymes acting on a single modified ba ...

    DNA glycosylases catalyze the excision of chemically modified bases from DNA. Although most glycosylases are specific to a particular base, the 3-methyladenine (m3A) DNA glycosylases include both highly specific enzymes acting on a single modified base, and enzymes with broader specificity for alkylation-damaged DNA. Our structural understanding of these different enzymatic specificities is currently limited to crystal and NMR structures of the unliganded enzymes and complexes with abasic DNA inhibitors. Presented here are high-resolution crystal structures of the m3A DNA glycosylase from Helicobacter pylori (MagIII) in the unliganded form and bound to alkylated bases 3,9-dimethyladenine and 1,N6-ethenoadenine. These are the first structures of a nucleobase bound in the active site of a m3A glycosylase belonging to the helix-hairpin-helix superfamily. MagIII achieves its specificity for positively-charged m3A not by direct interactions with purine or methyl substituent atoms, but rather by stacking the base between two aromatic side chains in a pocket that excludes 7-methylguanine. We report base excision and DNA binding activities of MagIII active site mutants, together with a structural comparison of the HhH glycosylases.


    Related Citations: 
    • A NOVEL 3-METHYLADENINE DNA GLYCOSYLASE FROM HELICOBACTER PYLORI DEFINES A NEW CLASS WITHIN THE ENDONUCLEASE III FAMILY OF BASE EXCISION REPAIR GLYCOSYLASES
      O'ROURKE, E.J.,CHEVALIER, C.,BOITEUX, S.,LABIGNE, A.,IELPI, L.,RADICELLA, J.P.
      (2000) J.Biol.Chem. 275: 20077


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-METHYLADENINE DNA GLYCOSYLASE
A, B
218Helicobacter pylori (strain ATCC 700392 / 26695)N/A
Find proteins for O25323 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25323
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EA1
Query on EA1

Download SDF File 
Download CCD File 
A, B
3H-IMIDAZO[2,1-I]PURINE
1,N6-ETHENOADENINE
C7 H5 N5
OGVOXGPIHFKUGM-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EA1Ki: 800000 nM BINDINGMOAD
EA1Ki: 800000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.605α = 90.00
b = 44.399β = 106.40
c = 81.516γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance