1MPG | pdb_00001mpg

3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI

• PDB DOI: https://doi.org/10.2210/pdb1MPG/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-10-28 Released: 1998-01-28 
• Deposition Author(s): Labahn, J., Schaerer, O.D., Long, A., Ezaz-Nikpay, K., Verdine, G.L., Ellenberger, T.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

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: 8706136 
• DOI: https://doi.org/10.1016/s0092-8674(00)80103-8
• Primary Citation Related Structures: 
  1MPG


• 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-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.

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Organizational Affiliation: 
• Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.03 kDa 
• Atom Count: 4,752 
• Modeled Residue Count: 564 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-METHYLADENINE DNA GLYCOSYLASE II	A, B	282	Escherichia coli	Mutation(s): 0  Gene Names: ALKA EC: 3.2.2.21
UniProt
Find proteins for P04395 (Escherichia coli (strain K12)) Explore P04395  Go to UniProtKB:  P04395

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.08	α = 90
b = 75.77	β = 109.94
c = 60.92	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Labahn, J., Schaerer, O.D., Long, A., Ezaz-Nikpay, K., Verdine, G.L., Ellenberger, T.E.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations