Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.79 kDa 
• Atom Count: 3729 
• Residue Count: 434 
• Unique protein chains: 1

1PU6

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII)

• DOI: 10.2210/pdb1PU6/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-06-24 Released: 2003-10-07 
• Deposition Author(s): Eichman, B.F., O'Rourke, E.J., Radicella, J.P., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.185 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

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

• PubMed: 14517230 
• DOI: 10.1093/emboj/cdg505
• Primary Citation of Related Structures:  
  1PU8, 1PU7, 1PU6


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-METHYLADENINE DNA GLYCOSYLASE	A, B	218	Helicobacter pylori	Mutation(s): 1
Find proteins for O25323 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25323  Go to UniProtKB:  O25323

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A,B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.185 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.605	α = 90
b = 44.399	β = 106.4
c = 81.516	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-24 
• Released Date: 2003-10-07 
Deposition Author(s): Eichman, B.F., O'Rourke, E.J., Radicella, J.P., Ellenberger, T.

Revision History 

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